Publications for New York Structural Genomics Research Consortium

Total Publications	184
Publications with >5 Citations	138
Structural Publications	87
Methodological and Other Publications	97
Total Citations	7665
Avg. Citations (Structural)	21.0
Avg. Citations (Methodological and Other)	60.2
Total Impact	1,165.5

More New York Structural Genomics Research Consortium statistics here.
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Structural Publications

2011 (click to unfold)

1. Target: NYSGXRC-11023l
   Bagaria A, Kumaran D, Burley SK, Swaminathan S 
   (2011)
   Structural basis for a ribofuranosyl binding protein: Insights into the furanose specific transport.
   Proteins, 79, 1352-7  (Details) (Pub Med ID: 21387413) (PDB: 3KSM)
   Times cited: 0
   


2. Wang L, Rubinstein R, Lines JL, Wasiuk A, Ahonen C, Guo Y, Lu LF, Gondek D, Wang Y, Fava RA, Fiser A, Almo S, Noelle RJ 
   (2011)
   VISTA, a novel mouse Ig superfamily ligand that negatively regulates T cell responses.
   Journal of Experimental Medicine, 208, 577-92  (Details) (Pub Med ID: 21383057)
   Times cited: no data
   


3. Target: NYSGXRC-9208a
   Kamat SS, Fan H, Sauder JM, Burley SK, Shoichet BK, Sali A, Raushel FM 
   (2011)
   Enzymatic deamination of the epigenetic base N-6-methyladenine.
   Journal of the American Chemical Society, 133, 2080-3  (Details) (Pub Med ID: 21275375)
   Times cited: no data
   


4. Target: NYSGXRC-9206a
   Kamat SS, Bagaria A, Kumaran D, Holmes-Hampton GP, Fan H, Sali A, Sauder JM, Burley SK, Lindahl PA, Swaminathan S, Raushel FM 
   (2011)
   Catalytic mechanism and three-dimensional structure of adenine deaminase.
   Biochemistry, 50, 1917-27  (Details) (Pub Med ID: 21247091)
   Times cited: 3
   


5. Target: NYSGXRC-11191g
   Zhang Z, Zhou R, Sauder JM, Tonge PJ, Burley SK, Swaminathan S 
   (2011)
   Structural and functional studies of fatty acyl adenylate ligases from E. coli and L. pneumophila.
   Journal of Molecular Biology, 406, 313-24  (Details) (Pub Med ID: 21185305)
   Times cited: 0
   



2010 (click to unfold)

6. Target: NYSGXRC-10196a
   Wisedchaisri G, Dranow DM, Lie TJ, Bonanno JB, Patskovsky Y, Ozyurt SA, Sauder JM, Almo SC, Wasserman SR, Burley SK, Leigh JA, Gonen T 
   (2010)
   Structural underpinnings of nitrogen regulation by the prototypical nitrogen-responsive transcriptional factor NrpR.
   Structure, 18, 1512-21  (Details) (Pub Med ID: 21070950) (PDB: 3NEK)
   Times cited: 1
   


7. Target: NYSGXRC-9501a
   Kikani CK, Antonysamy SA, Bonanno JB, Romero R, Zhang FF, Russell M, Gheyi T, Iizuka M, Emtage S, Sauder JM, Turk BE, Burley SK, Rutter J 
   (2010)
   Structural bases of PAS domain-regulated kinase (PASK) activation in the absence of activation loop phosphorylation.
   Journal of Biological Chemistry, 285, 41034-43  (Details) (Pub Med ID: 20943661) (PDB: 3DLS)
   Times cited: 2
   


8. Target: NYSGXRC-10383p
   Sampathkumar P, Lu F, Zhao X, Li Z, Gilmore J, Bain K, Rutter ME, Gheyi T, Schwinn KD, Bonanno JB, Pieper U, Fajardo JE, Fiser A, Almo SC, Swaminathan S, Chance MR, Baker D, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Sali A, Sauder JM, Burley SK 
   (2010)
   Structure of a putative BenF-like porin from Pseudomonas fluorescens Pf-5 at 2.6 A resolution.
   Proteins, 78, 3056-62  (Details) (Pub Med ID: 20737437) (PDB: 3JTY)
   Times cited: 2
   


9. Target: 9260c
   Xiang DF, Patskovsky Y, Xu C, Fedorov AA, Fedorov EV, Sisco AA, Sauder JM, Burley SK, Almo SC, Raushel FM 
   (2010)
   Functional identification and structure determination of two novel prolidases from cog1228 in the amidohydrolase superfamily .
   Biochemistry, 49, 6791-803  (Details) (Pub Med ID: 20604542) (PDB: 3MKV) (PDB: 3FEQ) (PDB: 3N2C)
   Times cited: 2
   


10. Target: NYSGXRC-9339a
    Hall RS, Agarwal R, Hitchcock D, Sauder JM, Burley SK, Swaminathan S, Raushel FM 
    (2010)
    Discovery and Structure Determination of the Orphan Enzyme Isoxanthopterin Deaminase .
    Biochemistry, 49, 4374-82  (Details) (Pub Med ID: 20415463) (PDB: 2PAJ)
    Times cited: 4
    


11. Target: NYSGXRC-15145a
    Sampathkumar P, Ozyurt SA, Do J, Bain KT, Dickey M, Rodgers LA, Gheyi T, Sali A, Kim SJ, Phillips J, Pieper U, Fernandez-Martinez J, Franke JD, Martel A, Tsuruta H, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Rout MP, Sauder JM, Burley SK 
    (2010)
    Structures of the autoproteolytic domain from the Saccharomyces cerevisiae nuclear pore complex component, Nup145.
    Proteins, 78, 1992-8  (Details) (Pub Med ID: 20310066) (PDB: 3KEP) (PDB: 3KES)
    Times cited: 2
    


12. Target: NYSGXRC-13170b
    Sampathkumar P, Ozyurt SA, Miller S, Bain KT, Rutter ME, Gheyi T, Abrams B, Wang Y, Atwell S, Luz JG, Thompson DA, Wasserman SR, Emtage JS, Park EC, Rongo C, Jin Y, Klemke RL, Sauder JM, Burley SK 
    (2010)
    Structures of PHR Domains from Mus musculus Phr1 (Mycbp2) Explain the Loss-of-Function Mutation (Gly1092-->Glu) of the C. elegans Ortholog RPM-1.
    Journal of Molecular Biology, 397, 883-92  (Details) (Pub Med ID: 20156452) (PDB: 3GBW) (PDB: 3HWJ)
    Times cited: 0
    


13. Target: NYSGXRC-9236e
    Hall RS, Fedorov AA, Marti-Arbona R, Fedorov EV, Kolb P, Sauder JM, Burley SK, Shoichet BK, Almo SC, Raushel FM 
    (2010)
    The hunt for 8-oxoguanine deaminase.
    Accounts of Chemical Research, 132, 1762-3  (Details) (Pub Med ID: 20088583) (PDB: 3H4U)
    Times cited: 8
    


14. Target: NYSGXRC-10278a
    Lakshminarasimhan D, Eswaramoorthy S, Burley SK, Swaminathan S 
    (2010)
    Structure of YqgQ protein from Bacillus subtilis, a conserved hypothetical protein.
    Acta Crystallographica Section F: Structural Biology and Crystallization Communications, 66, 8-11  (Details) (Pub Med ID: 20057058) (PDB: 2NN4)
    Times cited: 0
    



2009 (click to unfold)

15. Target: NYSGXRC-9375a
    Rakus JF, Kalyanaraman C, Fedorov AA, Fedorov EV, Mills-Groninger FP, Toro R, Bonanno J, Bain K, Sauder JM, Burley SK, Almo SC, Jacobson MP, Gerlt JA 
    (2009)
    Computation-Facilitated Assignment of the Function in the Enolase Superfamily: A Regiochemically Distinct Galactarate Dehydratase from Oceanobacillus iheyensis .
    Biochemistry, 48, 11546-58  (Details) (Pub Med ID: 19883118) (PDB: 2OQY)
    Times cited: 4
    


16. Target: NYSGXRC-10146c
    Sampaleanu LM, Bonanno JB, Ayers M, Koo J, Tammam S, Burley SK, Almo SC, Burrows LL, Howell PL 
    (2009)
    Periplasmic domains of Pseudomonas aeruginosa PilN and PilO form a stable heterodimeric complex.
    Journal of Molecular Biology, 394, 143-59  (Details) (Pub Med ID: 19857646) (PDB: 2RJZ)
    Times cited: 10
    


17. Target: NYSGXRC-9507a
    Kiser PD, Golczak M, Lodowski DT, Chance MR, Palczewski K 
    (2009)
    Crystal structure of native RPE65, the retinoid isomerase of the visual cycle.
    Proceedings of the National Academy of Sciences of the United States of America, 106, 17325-30  (Details) (Pub Med ID: 19805034) (PDB: 3FSN)
    Times cited: 23
    


18. Target: NYSGXRC-10001b
    Ragumani S, Sauder JM, Burley SK, Swaminathan S 
    (2009)
    Structural studies on cytosolic domain of magnesium transporter MgtE from Enterococcus faecalis.
    Proteins, 78, 487-91  (Details) (Pub Med ID: 19787770) (PDB: 2OUX)
    Times cited: no data
    


19. Target: NYSGXRC-9201a
    Alvarado JJ, Nemkal A, Sauder JM, Russell M, Akiyoshi DE, Shi W, Almo SC, Weiss LM 
    (2009)
    Structure of a microsporidian methionine aminopeptidase type 2 complexed with fumagillin and TNP-470.
    Molecular and Biochemical Parasitology, 168, 158-67  (Details) (Pub Med ID: 19660503) (PDB: 3FM3) (PDB: 3FMQ) (PDB: 3FMR)
    Times cited: 2
    


20. Xiang DF, Xu C, Kumaran D, Brown AC, Sauder JM, Burley SK, Swaminathan S, Raushel FM 
    (2009)
    Functional Annotation of Two New Carboxypeptidases from the Amidohydrolase Superfamily of Enzymes.
    Biochemistry, 48, 4567-76  (Details) (Pub Med ID: 19358546) (PDB: 2QS8)
    Times cited: 5
    


21. Xiang DF, Patskovsky Y, Xu C, Meyer AJ, Sauder JM, Burley SK, Almo SC, Raushel FM 
    (2009)
    Functional identification of incorrectly annotated prolidases from the amidohydrolase superfamily of enzymes.
    Biochemistry, 48, 3730-42  (Details) (Pub Med ID: 19281183) (PDB: 3BE7) (PDB: 3DUG)
    Times cited: 6
    


22. Leiman PG, Basler M, Ramagopal UA, Bonanno JB, Sauder JM, Pukatzki S, Burley SK, Almo SC, Mekalanos JJ 
    (2009)
    Type VI secretion apparatus and phage tail-associated protein complexes share a common evolutionary origin.
    Proceedings of the National Academy of Sciences of the United States of America, 106, 4154-9  (Details) (Pub Med ID: 19251641) (PDB: 2P5Z)
    Times cited: 59
    


23. Sakai A, Fedorov AA, Fedorov EV, Schnoes AM, Glasner ME, Brown S, Rutter ME, Bain K, Chang S, Gheyi T, Sauder JM, Burley SK, Babbitt PC, Almo SC, Gerlt JA 
    (2009)
    Evolution of enzymatic activities in the enolase superfamily: stereochemically distinct mechanisms in two families of cis,cis-muconate lactonizing enzymes.
    Biochemistry, 48, 1445-53  (Details) (Pub Med ID: 19220063) (PDB: 3DG3) (PDB: 3DG6) (PDB: 3DG7) (PDB: 3DGB) (PDB: 3CT2)
    Times cited: 4
    



2008 (click to unfold)

24. Rao KN, Burley SK, Swaminathan S 
    (2008)
    UPF201 archaeal specific family members reveal structural similarity to RNA-binding proteins but low likelihood for RNA-binding function.
    PLoS ONE, 3, e3903  (Details) (Pub Med ID: 19079550) (PDB: 2PZZ) (PDB: 2NRQ) (PDB: 2NWU) (PDB: 2OGK)
    Times cited: 0
    


25. Legler PM, Kumaran D, Swaminathan S, Studier FW, Millard CB 
    (2008)
    Structural characterization and reversal of the natural organophosphate resistance of a D-type esterase, Saccharomyces cerevisiae S-formylglutathione hydrolase.
    Biochemistry, 47, 9592-601  (Details) (Pub Med ID: 18707125) (PDB: 1PV1)
    Times cited: 7
    


26. Ragumani S, Kumaran D, Burley SK, Swaminathan S 
    (2008)
    Crystal structure of a putative lysostaphin peptidase from Vibrio cholerae.
    Proteins, 72, 1096-103  (Details) (Pub Med ID: 18498110) (PDB: 2GU1)
    Times cited: 4
    


27. Tyagi R, Eswaramoorthy S, Burley SK, Raushel FM, Swaminathan S 
    (2008)
    A common catalytic mechanism for proteins of the HutI family.
    Biochemistry, 47(20), 5608-15  (Details) (Pub Med ID: 18442260) (PDB: 2Q09)
    Times cited: 3
    


28. Agarwal R, Burley SK, Swaminathan S 
    (2008)
    A novel mode of dimerization via formation of a glutamate anhydride crosslink in a protein crystal structure.
    Proteins, 71(2), 1038-41  (Details) (Pub Med ID: 18247349) (PDB: 1SG9)
    Times cited: 0
    


29. Agarwal R, Burley SK, Swaminathan S 
    (2008)
    Structure of human dual specificity protein phosphatase 23, VHZ, enzyme-substrate/product complex.
    Journal of Biological Chemistry, 283(14), 8946-53  (Details) (Pub Med ID: 18245086) (PDB: 2IMG)
    Times cited: 7
    


30. Madegowda M, Eswaramoorthy S, Burley SK, Swaminathan S 
    (2008)
    X-ray crystal structure of the B component of Hemolysin BL from Bacillus cereus.
    Proteins, 71, 534-40  (Details) (Pub Med ID: 18175317) (PDB: 2NRJ)
    Times cited: 5
    


31. Rao KN, Burley SK, Swaminathan S 
    (2008)
    Crystal structure of a conserved protein of unknown function (MJ1651) from Methanococcus jannaschii.
    Proteins, 70(2), 572-7  (Details) (Pub Med ID: 17910070) (PDB: 2F4N)
    Times cited: 1
    



2007 (click to unfold)

32. Almo SC, Bonanno JB, Sauder JM, Emtage S, Dilorenzo TP, Malashkevich V, Wasserman SR, Swaminathan S, Eswaramoorthy S, Agarwal R, Kumaran D, Madegowda M, Ragumani S, Patskovsky Y, Alvarado J, Ramagopal UA, Faber-Barata J, Chance MR, Sali A, Fiser A, Zhang ZY, Lawrence DS, Burley SK 
    (2007)
    Structural genomics of protein phosphatases.
    Journal of Structural and Functional Genomics, 8(2-3), 121-40  (Details) (Pub Med ID: 18058037) (PDB: 2FH7)
    Times cited: 26
    


33. Tyagi R, Burley SK, Swaminathan S 
    (2007)
    X-ray structures of two proteins belonging to Pfam DUF178 revealed unexpected structural similarity to the DUF191 Pfam family.
    BMC Structural Biology, 7(6), 62  (Details) (Pub Med ID: 17908300) (PDB: 2I6E)
    Times cited: 1
    


34. Tyagi R, Kumaran D, Burley SK, Swaminathan S 
    (2007)
    X-ray structure of imidazolonepropionase from Agrobacterium tumefaciens at 1.87 A resolution.
    Proteins, 69(3), 652-8  (Details) (Pub Med ID: 17640072) (PDB: 2PUZ)
    Times cited: 2
    


35. Hermann JC, Marti-Arbona R, Fedorov AA, Fedorov E, Almo SC, Shoichet BK, Raushel FM 
    (2007)
    Structure-based activity prediction for an enzyme of unknown function.
    Nature, 448(7155), 775-9  (Details) (Pub Med ID: 17603473) (PDB: 2PLM)
    Times cited: 95
    


36. Velge P, Herler M, Johansson J, Roche SM, Témoin S, Fedorov AA, Gracieux P, Almo SC, Goebel W, Cossart P 
    (2007)
    A naturally occurring mutation K220T in the pleiotropic activator PrfA of Listeria monocytogenes results in a loss of virulence due to decreasing DNA-binding affinity.
    Microbiology, 153(Pt 4), 995-1005  (Details) (Pub Med ID: 17379709) (PDB: 1OMI)
    Times cited: 15
    


37. Agarwal R, Burley SK, Swaminathan S 
    (2007)
    Structural analysis of a ternary complex of allantoate amidohydrolase from Escherichia coli reveals its mechanics.
    Journal of Molecular Biology, 368(2), 450-63  (Details) (Pub Med ID: 17362992) (PDB: 1Z2L)
    Times cited: 14
    


38. Jefferson JJ, Ciatto C, Shapiro L, Liem RK 
    (2007)
    Structural analysis of the plakin domain of bullous pemphigoid antigen1 (BPAG1) suggests that plakins are members of the spectrin superfamily.
    Journal of Molecular Biology, 366(1), 244-57  (Details) (Pub Med ID: 17161423) (PDB: 2IAK)
    Times cited: 17
    



2006 (click to unfold)

39. Rao KN, Bonanno JB, Burley SK, Swaminathan S 
    (2006)
    Crystal structure of glycerophosphodiester phosphodiesterase from Agrobacterium tumefaciens by SAD with a large asymmetric unit.
    Proteins, 65(2), 514-8  (Details) (Pub Med ID: 16909422) (PDB: 1ZCC)
    Times cited: 7
    


40. Kumaran D, Bonanno JB, Burley SK, Swaminathan S 
    (2006)
    Crystal structure of phosphatidylglycerophosphatase (PGPase), a putative membrane-bound lipid phosphatase, reveals a novel binuclear metal binding site and two "proton wires".
    Proteins, 64(4), 851-62  (Details) (Pub Med ID: 16838328) (PDB: 1Y9I)
    Times cited: 3
    


41. Rao KN, Kumaran D, Seetharaman J, Bonanno JB, Burley SK, Swaminathan S 
    (2006)
    Crystal structure of trehalose-6-phosphate phosphatase-related protein: biochemical and biological implications.
    Protein Science, 15(7), 1735-44  (Details) (Pub Med ID: 16815921) (PDB: 1U02)
    Times cited: 8
    


42. Eswaramoorthy S, Bonanno JB, Burley SK, Swaminathan S 
    (2006)
    Mechanism of action of a flavin-containing monooxygenase.
    Proceedings of the National Academy of Sciences of the United States of America, 103(26), 9832-7  (Details) (Pub Med ID: 16777962) (PDB: 2GV8)
    Times cited: 40
    


43. Manjasetty BA, Chance MR 
    (2006)
    Crystal structure of Escherichia coli L-arabinose isomerase (ECAI), the putative target of biological tagatose production.
    Journal of Molecular Biology, 360(2), 297-309  (Details) (Pub Med ID: 16756997) (PDB: 2AJT)
    Times cited: 25
    


44. Agarwal R, Bonanno JB, Burley SK, Swaminathan S 
    (2006)
    Structure determination of an FMN reductase from Pseudomonas aeruginosa PA01 using sulfur anomalous signal.
    Acta Crystallographica Section D: Biological Crystallography, 62(Pt 4), 383-91  (Details) (Pub Med ID: 16552139) (PDB: 1RTT)
    Times cited: 18
    


45. Seetharaman J, Rajashankar KR, Solorzano V, Kniewel R, Lima CD, Bonanno JB, Burley SK, Swaminathan S 
    (2006)
    Crystal structures of two putative phosphoheptose isomerases.
    Proteins, 63(4), 1092-6  (Details) (Pub Med ID: 16477602) (PDB: 1TK9)
    Times cited: 7
    


46. Seetharaman J, Kumaran D, Bonanno JB, Burley SK, Swaminathan S 
    (2006)
    Crystal structure of a putative HTH-type transcriptional regulator yxaF from Bacillus subtilis.
    Proteins, 63(4), 1087-91  (Details) (Pub Med ID: 16475182) (PDB: 1SGM)
    Times cited: 3
    


47. Song F, Zhuang Z, Finci L, Dunaway-Mariano D, Kniewel R, Buglino JA, Solorzano V, Wu J, Lima CD 
    (2006)
    Structure, function, and mechanism of the phenylacetate pathway hot dog-fold thioesterase PaaI.
    Journal of Biological Chemistry, 281(16), 11028-38  (Details) (Pub Med ID: 16464851) (PDB: 2FS2)
    Times cited: 21
    


48. Bewley MC, Graziano V, Jiang J, Matz E, Studier FW, Pegg AE, Coleman CS, Flanagan JM 
    (2006)
    Structures of wild-type and mutant human spermidine/spermine N1-acetyltransferase, a potential therapeutic drug target.
    Proceedings of the National Academy of Sciences of the United States of America, 103(7), 2063-8  (Details) (Pub Med ID: 16455797) (PDB: 2B3U)
    Times cited: 18
    



2005 (click to unfold)

49. Zhan C, Fedorov EV, Shi W, Ramagopal UA, Thirumuruhan R, Manjasetty BA, Almo SC, Fiser A, Chance MR, Fedorov AA 
    (2005)
    The ybeY protein from Escherichia coli is a metalloprotein.
    Acta Crystallographica Section F: Structural Biology and Crystallization Communications, 61(Pt 11), 959-63  (Details) (Pub Med ID: 16511207) (PDB: 1XM5)
    Times cited: 9
    


50. Gorman J, Shapiro L 
    (2005)
    Crystal structures of the tryptophan repressor binding protein WrbA and complexes with flavin mononucleotide.
    Protein Science, 14(12), 3004-12  (Details) (Pub Med ID: 16322580) (PDB: 1YRH)
    Times cited: 12
    


51. Badger J, Sauder JM, Adams JM, Antonysamy S, Bain K, Bergseid MG, Buchanan SG, Buchanan MD, Batiyenko Y, Christopher JA, Emtage S, Eroshkina A, Feil I, Furlong EB, Gajiwala KS, Gao X, He D, Hendle J, Huber A, Hoda K, Kearins P, Kissinger C, Laubert B, Lewis HA, Lin J, Loomis K, Lorimer D, Louie G, Maletic M, Marsh CD, Miller I, Molinari J, Muller-Dieckmann HJ, Newman JM, Noland BW, Pagarigan B, Park F, Peat TS, Post KW, Radojicic S, Ramos A, Romero R, Rutter ME, Sanderson WE, Schwinn KD, Tresser J, Winhoven J, Wright TA, Wu L, Xu J, Harris TJ 
    (2005)
    Structural analysis of a set of proteins resulting from a bacterial genomics project.
    Proteins, 60(4), 787-96  (Details) (Pub Med ID: 16021622)
    Times cited: 85
    


52. Strokopytov BV, Fedorov A, Mahoney NM, Kessels M, Drubin DG, Almo SC 
    (2005)
    Phased translation function revisited: structure solution of the cofilin-homology domain from yeast actin-binding protein 1 using six-dimensional searches.
    Acta Crystallographica Section D: Biological Crystallography, 61(Pt 3), 285-93  (Details) (Pub Med ID: 15735338) (PDB: 1HQZ)
    Times cited: 14
    


53. Kumaran D, Eswaramoorthy S, Studier FW, Swaminathan S 
    (2005)
    Structure and mechanism of ADP-ribose-1'-monophosphatase (Appr-1'-pase), a ubiquitous cellular processing enzyme.
    Protein Science, 14(3), 719-26  (Details) (Pub Med ID: 15722447) (PDB: 1NJR)
    Times cited: 22
    


54. Sickmier EA, Brekasis D, Paranawithana S, Bonanno JB, Paget MS, Burley SK, Kielkopf CL 
    (2005)
    X-ray structure of a Rex-family repressor/NADH complex insights into the mechanism of redox sensing.
    Structure, 13(1), 43-54  (Details) (Pub Med ID: 15642260) (PDB: 1XCB)
    Times cited: 18
    



2004 (click to unfold)

55. Gorman J, Shapiro L 
    (2004)
    Structure of serine acetyltransferase from Haemophilus influenzae Rd.
    Acta Crystallographica Section D: Biological Crystallography, 60(Pt 9), 1600-5  (Details) (Pub Med ID: 15333931) (PDB: 1S80)
    Times cited: 14
    


56. Dodatko T, Fedorov AA, Grynberg M, Patskovsky Y, Rozwarski DA, Jaroszewski L, Aronoff-Spencer E, Kondraskina E, Irving T, Godzik A, Almo SC 
    (2004)
    Crystal structure of the actin binding domain of the cyclase-associated protein.
    Biochemistry, 43(33), 10628-41  (Details) (Pub Med ID: 15311924)
    Times cited: 18
    


57. Patel SD, Rajala MW, Rossetti L, Scherer PE, Shapiro L 
    (2004)
    Disulfide-dependent multimeric assembly of resistin family hormones.
    Science, 304(5674), 1154-8  (Details) (Pub Med ID: 15155948) (PDB: 1RH7)
    Times cited: 113
    


58. Mohri K, Vorobiev S, Fedorov AA, Almo SC, Ono S 
    (2004)
    Identification of functional residues on Caenorhabditis elegans actin-interacting protein 1 (UNC-78) for disassembly of actin depolymerizing factor/cofilin-bound actin filaments.
    Journal of Biological Chemistry, 279(30), 31697-707  (Details) (Pub Med ID: 15150269) (PDB: 1NR0)
    Times cited: 42
    


59. Buglino J, Onwueme KC, Ferreras JA, Quadri LE, Lima CD 
    (2004)
    Crystal structure of PapA5, a phthiocerol dimycocerosyl transferase from Mycobacterium tuberculosis.
    Journal of Biological Chemistry, 279(29), 30634-42  (Details) (Pub Med ID: 15123643) (PDB: 1Q9J)
    Times cited: 27
    


60. Daniels BV, Jiang JS, Fu D 
    (2004)
    Crystallization and preliminary crystallographic analysis of the Escherichia coli water channel AqpZ.
    Acta Crystallographica Section D: Biological Crystallography, 60(Pt 3), 561-3  (Details) (Pub Med ID: 14993693)
    Times cited: 5
    


61. Gogos A, Gorman J, Shapiro L 
    (2004)
    Structure of Escherichia coli YfdW, a type III CoA transferase.
    Acta Crystallographica Section D: Biological Crystallography, 60(Pt 3), 507-11  (Details) (Pub Med ID: 14993676) (PDB: 1Q7E)
    Times cited: 9
    


62. Fabrega C, Hausmann S, Shen V, Shuman S, Lima CD 
    (2004)
    Structure and mechanism of mRNA cap (guanine-N7) methyltransferase.
    Molecular Cell, 13(1), 77-89  (Details) (Pub Med ID: 14731396) (PDB: 1RI1)
    Times cited: 59
    


63. Deo RC, Schmidt EF, Elhabazi A, Togashi H, Burley SK, Strittmatter SM 
    (2004)
    Structural bases for CRMP function in plexin-dependent semaphorin3A signaling.
    EMBO Journal, 23(1), 9-22  (Details) (Pub Med ID: 14685275) (PDB: 1KCX)
    Times cited: 59
    



2003 (click to unfold)

64. Gogos A, Mu H, Bahna F, Gomez CA, Shapiro L 
    (2003)
    Crystal structure of YdcE protein from Bacillus subtilis.
    Proteins, 53(2), 320-2  (Details) (Pub Med ID: 14517982) (PDB: 1NE8)
    Times cited: 10
    


65. Padyana AK, Burley SK 
    (2003)
    Crystal structure of shikimate 5-dehydrogenase (SDH) bound to NADP: insights into function and evolution.
    Structure, 11(8), 1005-13  (Details) (Pub Med ID: 12906831) (PDB: 1NVT)
    Times cited: 21
    


66. Kumaran D, Eswaramoorthy S, Gerchman SE, Kycia H, Studier FW, Swaminathan S 
    (2003)
    Crystal structure of a putative CN hydrolase from yeast.
    Proteins, 52(2), 283-91  (Details) (Pub Med ID: 12833551) (PDB: 1F89)
    Times cited: 32
    


67. Kamada K, Hanaoka F, Burley SK 
    (2003)
    Crystal structure of the MazE/MazF complex: molecular bases of antidote-toxin recognition.
    Molecular Cell, 11(4), 875-84  (Details) (Pub Med ID: 12718874) (PDB: 1UB4)
    Times cited: 111
    


68. Eswaramoorthy S, Gerchman S, Graziano V, Kycia H, Studier FW, Swaminathan S 
    (2003)
    Structure of a yeast hypothetical protein selected by a structural genomics approach.
    Acta Crystallographica Section D: Biological Crystallography, 59(Pt 1), 127-35  (Details) (Pub Med ID: 12499548) (PDB: 1B54)
    Times cited: 13
    


69. Burling FT, Kniewel R, Buglino JA, Chadha T, Beckwith A, Lima CD 
    (2003)
    Structure of Escherichia coli uridine phosphorylase at 2.0 A.
    Acta Crystallographica Section D: Biological Crystallography, 59(Pt 1), 73-6  (Details) (Pub Med ID: 12499542) (PDB: 1LX7)
    Times cited: 20
    


70. Ray SS, Bonanno JB, Chen H, de Lencastre H, Wu S, Tomasz A, Burley SK 
    (2003)
    X-ray structure of an M. jannaschii DNA-binding protein: implications for antibiotic resistance in S. aureus.
    Proteins, 50(1), 170-3  (Details) (Pub Med ID: 12471609) (PDB: 1KU9)
    Times cited: 9
    


71. Shi W, Ostrov D, Gerchman S, Kycia H, Studier FW, Edstrom W, Bresnick A, Ehrlich J, Blanchard J, Almo S, Chance MR 
    (2003)
    High-Throughput Structural Biology and Proteomics
    Protein Arrays, Biochips and Proteomics: The Next Phase of Genomics Discovery, Marcel Dekker, Inc., New York, Chapter 12.Protein Arrays, Biochips and Proteomics: The Next Phase of Genomics Discovery, Marcel Dekker, Inc., New York, Chapter 12.  (Details)
    Times cited: no data
    



2002 (click to unfold)

72. Kniewel R, Buglino JA, Shen V, Chadha T, Beckwith A, Lima CD 
    (2002)
    Structural analysis of Saccharomyces cerevisiae myo-inositol phosphate synthase.
    Journal of Structural and Functional Genomics, 2(3), 129-34  (Details) (Pub Med ID: 12836703) (PDB: 1LA2)
    Times cited: 7
    


73. Gogos A, Shapiro L 
    (2002)
    Large conformational changes in the catalytic cycle of glutathione synthase.
    Structure, 10(12), 1669-76  (Details) (Pub Med ID: 12467574) (PDB: 1M0T)
    Times cited: 16
    


74. Buglino J, Shen V, Hakimian P, Lima CD 
    (2002)
    Structural and biochemical analysis of the Obg GTP binding protein.
    Structure, 10(11), 1581-92  (Details) (Pub Med ID: 12429099)
    Times cited: 62
    


75. Ray SS, Bonanno JB, Rajashankar KR, Pinho MG, He G, De Lencastre H, Tomasz A, Burley SK 
    (2002)
    Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor.
    Structure, 10(11), 1499-508  (Details) (Pub Med ID: 12429091) (PDB: 1TUF)
    Times cited: 23
    


76. Kielkopf CL, Burley SK 
    (2002)
    X-ray structures of threonine aldolase complexes: structural basis of substrate recognition.
    Biochemistry, 41(39), 11711-20  (Details) (Pub Med ID: 12269813) (PDB: 1LW4)
    Times cited: 15
    


77. Deaconescu AM, Roll-Mecak A, Bonanno JB, Gerchman SE, Kycia H, Studier FW, Burley SK 
    (2002)
    X-ray structure of Saccharomyces cerevisiae homologous mitochondrial matrix factor 1 (Hmf1).
    Proteins, 48(2), 431-6  (Details) (Pub Med ID: 12112709) (PDB: 1JD1)
    Times cited: 10
    


78. Romanowski MJ, Soccio RE, Breslow JL, Burley SK 
    (2002)
    Crystal structure of the Mus musculus cholesterol-regulated START protein 4 (StarD4) containing a StAR-related lipid transfer domain.
    Proceedings of the National Academy of Sciences of the United States of America, 99(10), 6949-54  (Details) (Pub Med ID: 12011453) (PDB: 1JSS)
    Times cited: 76
    


79. Romanowski MJ, Bonanno JB, Burley SK 
    (2002)
    Crystal structure of the Streptococcus pneumoniae phosphomevalonate kinase, a member of the GHMP kinase superfamily.
    Proteins, 47(4), 568-71  (Details) (Pub Med ID: 12001237) (PDB: 1K47)
    Times cited: 37
    


80. Romanowski MJ, Bonanno JB, Burley SK 
    (2002)
    Crystal structure of the Escherichia coli glucose-inhibited division protein B (GidB) reveals a methyltransferase fold.
    Proteins, 47(4), 563-7  (Details) (Pub Med ID: 12001236) (PDB: 1JSX)
    Times cited: 12
    


81. Romanowski MJ, Burley SK 
    (2002)
    Crystal structure of the Escherichia coli shikimate kinase I (AroK) that confers sensitivity to mecillinam.
    Proteins, 47(4), 558-62  (Details) (Pub Med ID: 12001235) (PDB: 1KAG)
    Times cited: 21
    


82. Romanowski MJ, Gibney SA, Burley SK 
    (2002)
    Crystal structure of the Escherichia coli SbmC protein that protects cells from the DNA replication inhibitor microcin B17.
    Proteins, 47(3), 403-7  (Details) (Pub Med ID: 11948793) (PDB: 1JYH)
    Times cited: 11
    


83. Chance MR, Bresnick AR, Burley SK, Jiang JS, Lima CD, Sali A, Almo SC, Bonanno JB, Buglino JA, Boulton S, Chen H, Eswar N, He G, Huang R, Ilyin V, McMahan L, Pieper U, Ray S, Vidal M, Wang LK 
    (2002)
    Structural genomics: a pipeline for providing structures for the biologist.
    Protein Science, 11(4), 723-38  (Details) (Pub Med ID: 11910018) (PDB: 1JR7)
    Times cited: 110
    


84. Lima CD 
    (2002)
    Analysis of the E. coli NifS CsdB protein at 2.0 A reveals the structural basis for perselenide and persulfide intermediate formation.
    Journal of Molecular Biology, 315(5), 1199-208  (Details) (Pub Med ID: 11827487) (PDB: 1KMJ)
    Times cited: 45
    



2001 (click to unfold)

85. Bonanno JB, Edo C, Eswar N, Pieper U, Romanowski MJ, Ilyin V, Gerchman SE, Kycia H, Studier FW, Sali A, Burley SK 
    (2001)
    Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis.
    Proceedings of the National Academy of Sciences of the United States of America, 98(23), 12896-901  (Details) (Pub Med ID: 11698677) (PDB: 1I9A)
    Times cited: 71
    


86. Kamada K, Shu F, Chen H, Malik S, Stelzer G, Roeder RG, Meisterernst M, Burley SK 
    (2001)
    Crystal structure of negative cofactor 2 recognizing the TBP-DNA transcription complex.
    Cell, 106(1), 71-81  (Details) (Pub Med ID: 11461703) (PDB: 1JFI)
    Times cited: 73
    



2000 (click to unfold)

87. Groft CM, Beckmann R, Sali A, Burley SK 
    (2000)
    Crystal structures of ribosome anti-association factor IF6.
    Nature Structural & Molecular Biology, 7(12), 1156-64  (Details) (Pub Med ID: 11101899) (PDB: 1G62)
    Times cited: 30
    

Total number of citations for structural publications: 1825
Average number of citations per publication (structural): 21.0

Methodological and Other Publications

2011 (click to unfold)

1. Chruszcz M, Maleki SJ, Majorek KA, Demas M, Bublin M, Solberg R, Hurlburt BK, Ruan S, Mattisohn CP, Breiteneder H, Minor W 
   (2011)
   Structural and Immunologic Characterization of Ara h 1, a Major Peanut Allergen.
   Journal of Biological Chemistry, 286, 39318-27  (Details) (Pub Med ID: 21917921)
   Times cited: 1
   


2. Cooper DR, Porebski PJ, Chruszcz M, Minor W 
   (2011)
   X-ray crystallography: Assessment and validation of protein-small molecule complexes for drug discovery.
   Expert Opin Drug Discov, 6, 771-782  (Details) (Pub Med ID: 21779303)
   Times cited: 0
   


3. Shi W, Chance MR 
   (2011)
   Metalloproteomics: forward and reverse approaches in metalloprotein structural and functional characterization.
   Current Opinion in Chemical Biology, 15, 144-8  (Details) (Pub Med ID: 21130021)
   Times cited: 1
   



2010 (click to unfold)

4. Pieper U, Webb BM, Barkan DT, Schneidman-Duhovny D, Schlessinger A, Braberg H, Yang Z, Meng EC, Pettersen EF, Huang CC, Datta RS, Sampathkumar P, Madhusudhan MS, Sjölander K, Ferrin TE, Burley SK, Sali A 
   (2010)
   ModBase, a database of annotated comparative protein structure models, and associated resources.
   Nucleic Acids Research, 39, D465-74  (Details) (Pub Med ID: 21097780)
   Times cited: no data
   


5. Gheyi T, Rodgers L, Romero R, Sauder JM, Burley SK 
   (2010)
   Mass spectrometry guided in situ proteolysis to obtain crystals for X-ray structure determination.
   Journal of the American Society for Mass Spectrometry, 21, 1795-801  (Details) (Pub Med ID: 20685133)
   Times cited: 1
   



2009 (click to unfold)

6. Pieper U, Chiang R, Seffernick JJ, Brown SD, Glasner ME, Kelly L, Eswar N, Sauder JM, Bonanno JB, Swaminathan S, Burley SK, Zheng X, Chance MR, Almo SC, Gerlt JA, Raushel FM, Jacobson MP, Babbitt PC, Sali A 
   (2009)
   Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies.
   Journal of Structural and Functional Genomics, 10, 107-25  (Details) (Pub Med ID: 19219566)
   Times cited: 7
   


7. Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL, Fidelis K, Fiser A, Godzik A, Huang YJ, Humblet C, Jacobson MP, Joachimiak A, Krystek SR, Kortemme T, Kryshtafovych A, Montelione GT, Moult J, Murray D, Sanchez R, Sosnick TR, Standley DM, Stouch T, Vajda S, Vasquez M, Westbrook JD, Wilson IA 
   (2009)
   Outcome of a workshop on applications of protein models in biomedical research.
   Structure, 17, 151-9  (Details) (Pub Med ID: 19217386)
   Times cited: 26
   


8. Nair R, Liu J, Soong TT, Acton TB, Everett JK, Kouranov A, Fiser A, Godzik A, Jaroszewski L, Orengo C, Montelione GT, Rost B 
   (2009)
   Structural genomics is the largest contributor of novel structural leverage.
   Journal of Structural and Functional Genomics, 10, 181-91  (Details) (Pub Med ID: 19194785)
   Times cited: 28
   



2008 (click to unfold)

9. Rykunov D, Steinberger E, Madrid-Aliste CJ, Fiser A 
   (2008)
   Improved scoring function for comparative modeling using the M4T method.
   Journal of Structural and Functional Genomics, 10, 95-9  (Details) (Pub Med ID: 18985440)
   Times cited: no data
   


10. Pieper U, Eswar N, Webb BM, Eramian D, Kelly L, Barkan DT, Carter H, Mankoo P, Karchin R, Marti-Renom MA, Davis FP, Sali A 
    (2008)
    MODBASE, a database of annotated comparative protein structure models and associated resources.
    Nucleic Acids Research, 37, D347-54  (Details) (Pub Med ID: 18948282)
    Times cited: no data
    


11. Agüero F, Al-Lazikani B, Aslett M, Berriman M, Buckner FS, Campbell RK, Carmona S, Carruthers IM, Chan AW, Chen F, Crowther GJ, Doyle MA, Hertz-Fowler C, Hopkins AL, McAllister G, Nwaka S, Overington JP, Pain A, Paolini GV, Pieper U, Ralph SA, Riechers A, Roos DS, Sali A, Shanmugam D, Suzuki T, Van Voorhis WC, Verlinde CL 
    (2008)
    Genomic-scale prioritization of drug targets: the TDR Targets database.
    Nature reviews. Drug discovery, 7, 900-7  (Details) (Pub Med ID: 18927591)
    Times cited: 74
    


12. Eramian D, Eswar N, Shen MY, Sali A 
    (2008)
    How well can the accuracy of comparative protein structure models be predicted?
    Protein Science, 17, 1881-93  (Details) (Pub Med ID: 18832340)
    Times cited: 24
    


13. Chiang RA, Sali A, Babbitt PC 
    (2008)
    Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies.
    PLoS Computational Biology, 4, e1000142  (Details) (Pub Med ID: 18670595)
    Times cited: 13
    


14. Shi W, Chance MR 
    (2008)
    Metallomics and metalloproteomics.
    Cellular and Molecular Life Science, 65, 3040-8  (Details) (Pub Med ID: 18560755)
    Times cited: 52
    


15. Sauder MJ, Rutter ME, Bain K, Rooney I, Gheyi T, Atwell S, Thompson DA, Emtage S, Burley SK 
    (2008)
    High throughput protein production and crystallization at NYSGXRC.
    Methods in Molecular Biology, 426, 561-75  (Details) (Pub Med ID: 18542890)
    Times cited: 7
    


16. Eswar N, Eramian D, Webb B, Shen MY, Sali A 
    (2008)
    Protein structure modeling with MODELLER.
    Methods in Molecular Biology, 426, 145-59  (Details) (Pub Med ID: 18542861)
    Times cited: 150
    


17. Espadaler J, Eswar N, Querol E, Avilés FX, Sali A, Marti-Renom MA, Oliva B 
    (2008)
    Prediction of enzyme function by combining sequence similarity and protein interactions.
    BMC Bioinformatics, 9, 249  (Details) (Pub Med ID: 18505562)
    Times cited: 8
    


18. Topf M, Lasker K, Webb B, Wolfson H, Chiu W, Sali A 
    (2008)
    Protein structure fitting and refinement guided by cryo-EM density.
    Structure, 16(2), 295-307  (Details) (Pub Med ID: 18275820)
    Times cited: 58
    


19. Structural Genomics Consortium; Architecture et Fonction des Macromolécules Biologiques; Berkeley Structural Genomics Center; China Structural Genomics Consortium; Integrated Center for Structure and Function Innovation; Israel Structural Proteomics Center; Joint Center for Structural Genomics; Midwest Center for Structural Genomics; New York Structural GenomiX Research Center for Structural Genomics; Northeast Structural Genomics Consortium; Oxford Protein Production Facility; Protein Sample Production Facility, Max Delbrück Center for Molecular Medicine; RIKEN Structural Genomics/Proteomics Initiative; SPINE2-Complexes 
    (2008)
    Protein production and purification.
    Nature Methods, 5, 135-46  (Details) (Pub Med ID: 18235434)
    Times cited: 75
    


20. Manjasetty BA, Turnbull AP, Panjikar S, Büssow K, Chance MR 
    (2008)
    Automated technologies and novel techniques to accelerate protein crystallography for structural genomics.
    Proteomics, 8(4), 612-25  (Details) (Pub Med ID: 18210369)
    Times cited: 23
    


21. Burley SK, Joachimiak A, Montelione GT, Wilson IA 
    (2008)
    Contributions to the NIH-NIGMS Protein Structure Initiative from the PSI Production Centers
    Structure, 16(1), 5-11  (Details) (Pub Med ID: 18184575)
    Times cited: 28
    



2007 (click to unfold)

22. Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A 
    (2007)
    Comparative protein structure modeling using MODELLER.
    Current Protocols in Protein Science, Chapter 2(11), Unit 2  (Details) (Pub Med ID: 18429317)
    Times cited: 0
    


23. Sali A, Lima CD, Kostic M 
    (2007)
    Structural genomics.
    Structure, 15(11), 1341  (Details) (Pub Med ID: 17997955)
    Times cited: 2
    


24. Davis FP, Barkan DT, Eswar N, McKerrow JH, Sali A 
    (2007)
    Host pathogen protein interactions predicted by comparative modeling.
    Protein Science, 16(12), 2585-96  (Details) (Pub Med ID: 17965183)
    Times cited: 26
    


25. Melo F, Sali A 
    (2007)
    Fold assessment for comparative protein structure modeling.
    Protein Science, 16(11), 2412-26  (Details) (Pub Med ID: 17905832)
    Times cited: 19
    


26. Feyfant E, Sali A, Fiser A 
    (2007)
    Modeling mutations in protein structures.
    Protein Science, 16(9), 2030-41  (Details) (Pub Med ID: 17766392)
    Times cited: 16
    


27. Marti-Renom MA, Rossi A, Al-Shahrour F, Davis FP, Pieper U, Dopazo J, Sali A 
    (2007)
    The AnnoLite and AnnoLyze programs for comparative annotation of protein structures.
    BMC Bioinformatics, 8 Suppl 4(2), S4  (Details) (Pub Med ID: 17570147)
    Times cited: 14
    


28. Marti-Renom MA, Pieper U, Madhusudhan MS, Rossi A, Eswar N, Davis FP, Al-Shahrour F, Dopazo J, Sali A 
    (2007)
    DBAli tools: mining the protein structure space.
    Nucleic Acids Research, 35(Web Server issue), W393-7  (Details) (Pub Med ID: 17478513)
    Times cited: 15
    


29. Rajashankar KR, Chance MR, Burley SK, Jiang J, Almo SC, Bresnick A, Huang R, He G, Chen H, Sullivan M, Toomey J, Radhakannan T, Franklin W, Sali A, Pieper U, McMahan L 
    (2007)
    Structural Genomics at the National Synchrotron Light Source
    2001 National Synchrotron Light Source Activity Report, 2-28 to 2-32., 28, 105-28  (Details) (Pub Med ID: 17153936)
    Times cited: no data
    


30. Manjasetty BA, Shi W, Zhan C, Fiser A, Chance MR 
    (2007)
    A high-throughput approach to protein structure analysis.
    Genetic Engineering, 28, 105-28  (Details) (Pub Med ID: 17153936)
    Times cited: 7
    



2006 (click to unfold)

31. Korkin D, Davis FP, Alber F, Luong T, Shen MY, Lucic V, Kennedy MB, Sali A 
    (2006)
    Structural modeling of protein interactions by analogy: application to PSD-95.
    PLoS Computational Biology, 2(11), e153  (Details) (Pub Med ID: 17096593)
    Times cited: 19
    


32. Shen MY, Sali A 
    (2006)
    Statistical potential for assessment and prediction of protein structures.
    Protein Science, 15(11), 2507-24  (Details) (Pub Med ID: 17075131)
    Times cited: 261
    


33. Colubri A, Jha AK, Shen MY, Sali A, Berry RS, Sosnick TR, Freed KF 
    (2006)
    Minimalist representations and the importance of nearest neighbor effects in protein folding simulations.
    Journal of Molecular Biology, 363(4), 835-57  (Details) (Pub Med ID: 16982067)
    Times cited: 16
    


34. Rossi A, Marti-Renom MA, Sali A 
    (2006)
    Localization of binding sites in protein structures by optimization of a composite scoring function.
    Protein Science, 15(10), 2366-80  (Details) (Pub Med ID: 16963645)
    Times cited: 10
    


35. Berman HM, Burley SK, Chiu W, Sali A, Adzhubei A, Bourne PE, Bryant SH, Dunbrack RL, Fidelis K, Frank J, Godzik A, Henrick K, Joachimiak A, Heymann B, Jones D, Markley JL, Moult J, Montelione GT, Orengo C, Rossmann MG, Rost B, Saibil H, Schwede T, Standley DM, Westbrook JD 
    (2006)
    Outcome of a workshop on archiving structural models of biological macromolecules.
    Structure, 14, 1211-7  (Details) (Pub Med ID: 16955948) (PDB: )
    Times cited: 15
    


36. Rai BK, Madrid-Aliste CJ, Fajardo JE, Fiser A 
    (2006)
    MMM: a sequence-to-structure alignment protocol.
    Bioinformatics, 22(21), 2691-2  (Details) (Pub Med ID: 16928737)
    Times cited: 12
    


37. Fernandez-Fuentes N, Zhai J, Fiser A 
    (2006)
    ArchPRED: a template based loop structure prediction server.
    Nucleic Acids Research, 34(Web Server issue), W173-6  (Details) (Pub Med ID: 16844985)
    Times cited: 18
    


38. Fernandez-Fuentes N, Fiser A 
    (2006)
    Saturating representation of loop conformational fragments in structure databanks.
    BMC Structural Biology, 6(7), 15  (Details) (Pub Med ID: 16820050)
    Times cited: 10
    


39. Eramian D, Shen MY, Devos D, Melo F, Sali A, Marti-Renom MA 
    (2006)
    A composite score for predicting errors in protein structure models.
    Protein Science, 15(7), 1653-66  (Details) (Pub Med ID: 16751606)
    Times cited: 70
    


40. Davis FP, Braberg H, Shen MY, Pieper U, Sali A, Madhusudhan MS 
    (2006)
    Protein complex compositions predicted by structural similarity.
    Nucleic Acids Research, 34(10), 2943-52  (Details) (Pub Med ID: 16738133)
    Times cited: 22
    


41. Fernandez-Fuentes N, Oliva B, Fiser A 
    (2006)
    A supersecondary structure library and search algorithm for modeling loops in protein structures.
    Nucleic Acids Research, 34(7), 2085-97  (Details) (Pub Med ID: 16617149)
    Times cited: 22
    


42. Chiu W, Baker ML, Almo SC 
    (2006)
    Structural biology of cellular machines.
    Trends in Cell Biology, 16(3), 144-50  (Details) (Pub Med ID: 16459078)
    Times cited: 27
    


43. Rai BK, Fiser A 
    (2006)
    Multiple mapping method: a novel approach to the sequence-to-structure alignment problem in comparative protein structure modeling.
    Proteins, 63(3), 644-61  (Details) (Pub Med ID: 16437570)
    Times cited: 30
    


44. Madhusudhan MS, Marti-Renom MA, Sanchez R, Sali A 
    (2006)
    Variable gap penalty for protein sequence-structure alignment.
    Protein Engineering, Design and Selection, 19(3), 129-33  (Details) (Pub Med ID: 16423846)
    Times cited: 22
    


45. Pieper U, Eswar N, Davis FP, Braberg H, Madhusudhan MS, Rossi A, Marti-Renom M, Karchin R, Webb BM, Eramian D, Shen MY, Kelly L, Melo F, Sali A 
    (2006)
    MODBASE: a database of annotated comparative protein structure models and associated resources.
    Nucleic Acids Research, 34(Database issue), D291-5  (Details) (Pub Med ID: 16381869)
    Times cited: 137
    


46. Eswar N, Marti-Renom MA 
    (2006)
    Comparative Protein Structure Modeling with MODELLER
    Current Protocols in Bioinformatics, I. John Wiley & Sons, ed.Current Protocols in Bioinformatics, I. John Wiley & Sons, ed.  (Details)
    Times cited: 0
    


47. Eswar N, Sali A 
    (2006)
    Comparative Modeling of Drug Target Proteins
    Comprehensive Medicinal Chemistry, J. Taylor, and D. Triggle, eds. (Elsevier).Comprehensive Medicinal Chemistry, J. Taylor, and D. Triggle, eds. (Elsevier).  (Details)
    Times cited: no data
    


48. Shi W, Chance MR 
    (2006)
    Structural Genomics: high-throughput methods in structure determination of protein domains
    Comprehensive Medicinal Chemistry II, Volume 3: Drug Discovery Technologies, C. Hansch, Ed., ElsevierComprehensive Medicinal Chemistry II, Volume 3: Drug Discovery Technologies, C. Hansch, Ed., Elsevier  (Details)
    Times cited: no data
    



2005 (click to unfold)

49. Shi W, Zhan C, Ignatov A, Manjasetty BA, Marinkovic N, Sullivan M, Huang R, Chance MR 
    (2005)
    Metalloproteomics: high-throughput structural and functional annotation of proteins in structural genomics.
    Structure, 13(10), 1473-86  (Details) (Pub Med ID: 16216579)
    Times cited: 46
    


50. Bonanno JB, Almo SC, Bresnick A, Chance MR, Fiser A, Swaminathan S, Jiang J, Studier FW, Shapiro L, Lima CD, Gaasterland TM, Sali A, Bain K, Feil I, Gao X, Lorimer D, Ramos A, Sauder JM, Wasserman SR, Emtage S, D'Amico KL, Burley SK 
    (2005)
    New York-Structural GenomiX Research Consortium (NYSGXRC): a large scale center for the protein structure initiative.
    Journal of Structural and Functional Genomics, 6(2-3), 225-32  (Details) (Pub Med ID: 16211523)
    Times cited: 20
    


51. Gao X, Bain K, Bonanno JB, Buchanan M, Henderson D, Lorimer D, Marsh C, Reynes JA, Sauder JM, Schwinn K, Thai C, Burley SK 
    (2005)
    High-throughput limited proteolysis/mass spectrometry for protein domain elucidation.
    Journal of Structural and Functional Genomics, 6(2-3), 129-34  (Details) (Pub Med ID: 16211509)
    Times cited: 29
    


52. Ramagopal UA, Dauter Z, Thirumuruhan R, Fedorov E, Almo SC 
    (2005)
    Radiation-induced site-specific damage of mercury derivatives: phasing and implications.
    Acta Crystallographica Section D: Biological Crystallography, 61(Pt 9), 1289-98  (Details) (Pub Med ID: 16131763)
    Times cited: 25
    


53. Studier FW 
    (2005)
    Protein production by auto-induction in high density shaking cultures.
    Protein Expression and Purification, 41(1), 207-34  (Details) (Pub Med ID: 15915565)
    Times cited: 911
    


54. Pellegrini O, Mathy N, Gogos A, Shapiro L, Condon C 
    (2005)
    The Bacillus subtilis ydcDE operon encodes an endoribonuclease of the MazF/PemK family and its inhibitor.
    Molecular Microbiology, 56(5), 1139-48  (Details) (Pub Med ID: 15882409)
    Times cited: 25
    


55. Karchin R, Diekhans M, Kelly L, Thomas DJ, Pieper U, Eswar N, Haussler D, Sali A 
    (2005)
    LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources.
    Bioinformatics, 21(12), 2814-20  (Details) (Pub Med ID: 15827081)
    Times cited: 96
    


56. Snell EH, van der Woerd MJ, Miller MD, Deacon AM 
    (2005)
    Finding a cold needle in a warm haystack: infrared imaging applied to locating crycocooled crystals in loops
    Journal of Applied Crystallography, 38, 69-77  (Details)
    Times cited: 7
    


57. Sauder JM, Rutter ME, Bain K, Rooney I, Gheyi T, Atwell S, Thompson DA, Emtage S, Burley SK 
    (2005)
    Comparative Protein Structure Modeling
    The Proteomics Protocols Handbook. Ed: J.M. Walker. Humana Press Inc., Totowa, NJ.The Proteomics Protocols Handbook. Ed: J.M. Walker. Humana Press Inc., Totowa, NJ.  (Details)
    Times cited: no data
    



2004 (click to unfold)

58. Chance MR, Fiser A, Sali A, Pieper U, Eswar N, Xu G, Fajardo JE, Radhakannan T, Marinkovic N 
    (2004)
    High-throughput computational and experimental techniques in structural genomics.
    Genome Research, 14(10B), 2145-54  (Details) (Pub Med ID: 15489337)
    Times cited: 45
    


59. Mancia F, Patel SD, Rajala MW, Scherer PE, Nemes A, Schieren I, Hendrickson WA, Shapiro L 
    (2004)
    Optimization of protein production in mammalian cells with a coexpressed fluorescent marker.
    Structure, 12(8), 1355-60  (Details) (Pub Med ID: 15296729)
    Times cited: 29
    


60. Jiang J, Sweet RM 
    (2004)
    Protein Data Bank depositions from synchrotron sources.
    Journal of Synchrotron Radiation, 11(Pt 4), 319-27  (Details) (Pub Med ID: 15211038)
    Times cited: 18
    


61. Rossi A, Deveraux Q, Turk B, Sali A 
    (2004)
    Comprehensive search for cysteine cathepsins in the human genome.
    Biological Chemistry, 385(5), 363-72  (Details) (Pub Med ID: 15195995)
    Times cited: 23
    


62. Mirkovic N, Marti-Renom MA, Weber BL, Sali A, Monteiro AN 
    (2004)
    Structure-based assessment of missense mutations in human BRCA1: implications for breast and ovarian cancer predisposition.
    Cancer Research, 64(11), 3790-7  (Details) (Pub Med ID: 15172985)
    Times cited: 55
    


63. Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A, Webb B, Greenblatt D, Huang CC, Ferrin TE, Sali A 
    (2004)
    MODBASE, a database of annotated comparative protein structure models, and associated resources.
    Nucleic Acids Research, 32(Database issue), D217-22  (Details) (Pub Med ID: 14681398)
    Times cited: 118
    



2003 (click to unfold)

64. Fiser A, Sali A 
    (2003)
    Modeller: generation and refinement of homology-based protein structure models.
    Methods in Enzymology, 374(Pt 7), 461-91  (Details) (Pub Med ID: 14696385)
    Times cited: 316
    


65. Huang RY, Boulton SJ, Vidal M, Almo SC, Bresnick AR, Chance MR 
    (2003)
    High-throughput expression, purification, and characterization of recombinant Caenorhabditis elegans proteins.
    Biochemical and Biophysical Research Communications, 307(4), 928-34  (Details) (Pub Med ID: 12878200)
    Times cited: 15
    


66. John B, Sali A 
    (2003)
    Comparative protein structure modeling by iterative alignment, model building and model assessment.
    Nucleic Acids Research, 31(14), 3982-92  (Details) (Pub Med ID: 12853614)
    Times cited: 108
    


67. Eswar N, John B, Mirkovic N, Fiser A, Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, Madhusudhan MS, Yerkovich B, Sali A 
    (2003)
    Tools for comparative protein structure modeling and analysis.
    Nucleic Acids Research, 31(13), 3375-80  (Details) (Pub Med ID: 12824331)
    Times cited: 142
    


68. Koh IY, Eyrich VA, Marti-Renom MA, Przybylski D, Madhusudhan MS, Eswar N, Graña O, Pazos F, Valencia A, Sali A, Rost B 
    (2003)
    EVA: Evaluation of protein structure prediction servers.
    Nucleic Acids Research, 31(13), 3311-5  (Details) (Pub Med ID: 12824315)
    Times cited: 100
    


69. Gao H, Sengupta J, Valle M, Korostelev A, Eswar N, Stagg SM, Van Roey P, Agrawal RK, Harvey SC, Sali A, Chapman MS, Frank J 
    (2003)
    Study of the structural dynamics of the E coli 70S ribosome using real-space refinement.
    Cell, 113(6), 789-801  (Details) (Pub Med ID: 12809609)
    Times cited: 189
    


70. Reboul J, Vaglio P, Rual JF, Lamesch P, Martinez M, Armstrong CM, Li S, Jacotot L, Bertin N, Janky R, Moore T, Hudson JR, Hartley JL, Brasch MA, Vandenhaute J, Boulton S, Endress GA, Jenna S, Chevet E, Papasotiropoulos V, Tolias PP, Ptacek J, Snyder M, Huang R, Chance MR, Lee H, Doucette-Stamm L, Hill DE, Vidal M 
    (2003)
    C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression.
    Nature Genetics, 34(1), 35-41  (Details) (Pub Med ID: 12679813)
    Times cited: 215
    


71. Burley SK, Bonanno JB 
    (2003)
    Structural genomics.
    Methods of Biochemical Analysis, 44(2-3), 591-612  (Details) (Pub Med ID: 12647406)
    Times cited: 22
    


72. Sali A, Glaeser R, Earnest T, Baumeister W 
    (2003)
    From words to literature in structural proteomics.
    Nature, 422(6928), 216-25  (Details) (Pub Med ID: 12634795)
    Times cited: 254
    


73. Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, McMahan L, Sali A 
    (2003)
    ModView, visualization of multiple protein sequences and structures.
    Bioinformatics, 19(1), 165-6  (Details) (Pub Med ID: 12499313)
    Times cited: 7
    


74. Pilloff D, Dabovic K, Romanowski MJ, Bonanno JB, Doherty M, Burley SK, Leyh TS 
    (2003)
    The kinetic mechanism of phosphomevalonate kinase.
    Journal of Biological Chemistry, 278(7), 4510-5  (Details) (Pub Med ID: 12424232)
    Times cited: 25
    


75. Marti-Renom MA, Fiser A, Madhusudhan MS, John B, Stuart A, Eswar N, Pieper P, Shen MY, Sali A 
    (2003)
    Modeling protein structure from its sequence
    Current Protocols in Bioinformatics John Wiley & Sons, Inc., V. 5 November Issue.Current Protocols in Bioinformatics John Wiley & Sons, Inc., V. 5 November Issue.  (Details)
    Times cited: no data
    



2002 (click to unfold)

76. Burley SK, Bonanno JB 
    (2002)
    Structuring the universe of proteins.
    Annual Review of Genomics and Human Genetics, 3(12), 243-62  (Details) (Pub Med ID: 12194989)
    Times cited: 40
    


77. Burley SK, Bonanno JB 
    (2002)
    Structural genomics of proteins from conserved biochemical pathways and processes.
    Current Opinion in Structural Biology, 12(3), 383-91  (Details) (Pub Med ID: 12127459)
    Times cited: 24
    


78. Fiser A, Feig M, Brooks CL, Sali A 
    (2002)
    Evolution and physics in comparative protein structure modeling.
    Accounts of Chemical Research, 35(6), 413-21  (Details) (Pub Med ID: 12069626)
    Times cited: 57
    


79. Soccio RE, Adams RM, Romanowski MJ, Sehayek E, Burley SK, Breslow JL 
    (2002)
    The cholesterol-regulated StarD4 gene encodes a StAR-related lipid transfer protein with two closely related homologues, StarD5 and StarD6.
    Proceedings of the National Academy of Sciences of the United States of America, 99(10), 6943-8  (Details) (Pub Med ID: 12011452)
    Times cited: 76
    


80. Marti-Renom MA, Madhusudhan MS, Fiser A, Rost B, Sali A 
    (2002)
    Reliability of assessment of protein structure prediction methods.
    Structure, 10(3), 435-40  (Details) (Pub Med ID: 12005441)
    Times cited: 52
    


81. Yang Y, Li L, Wong GW, Krilis SA, Madhusudhan MS, Sali A, Stevens RL 
    (2002)
    RasGRP4, a new mast cell-restricted Ras guanine nucleotide-releasing protein with calcium- and diacylglycerol-binding motifs. Identification of defective variants of this signaling protein in asthma, mastocytosis, and mast cell leukemia patients and demonstration of the importance of RasGRP4 in mast cell development and function.
    Journal of Biological Chemistry, 277(28), 25756-74  (Details) (Pub Med ID: 11956218)
    Times cited: 59
    


82. Stuart AC, Ilyin VA, Sali A 
    (2002)
    LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures.
    Bioinformatics, 18(1), 200-1  (Details) (Pub Med ID: 11836232)
    Times cited: 47
    


83. Melo F, Sánchez R, Sali A 
    (2002)
    Statistical potentials for fold assessment.
    Protein Science, 11(2), 430-48  (Details) (Pub Med ID: 11790853)
    Times cited: 120
    


84. Pieper U, Eswar N, Stuart AC, Ilyin VA, Sali A 
    (2002)
    MODBASE, a database of annotated comparative protein structure models.
    Nucleic Acids Research, 30(1), 255-9  (Details) (Pub Med ID: 11752309)
    Times cited: 65
    


85. Sauder JM, Rutter ME, Bain K, Rooney I, Gheyi T, Atwell S, Thompson DA, Emtage S and Burley SK 
    (2002)
    Comparative protein structure prediction
    Ed: John Wiley & Sons, Inc. Curr. Protocol. Prot. Sci. 1, 2.9.1-2.9.22.Ed: John Wiley & Sons, Inc. Curr. Protocol. Prot. Sci. 1, 2.9.1-2.9.22.  (Details)
    Times cited: no data
    


86. Sali A, Marti-Renom MA, Madhusudhan MS, Fiser A, Rost B 
    (2002)
    Reply to Moult et al
    Structure, 10, 292-293  (Details)
    Times cited: no data
    



2001 (click to unfold)

87. Gunther CS, Gaasterland T 
    (2001)
    Characterizing the relationship between protein-fusion and gene co-expression.
    Genome Informatics. International Conference on Genome Informatics, 12(Pt 2), 34-43  (Details) (Pub Med ID: 11791222)
    Times cited: 0
    


88. Spahn CM, Beckmann R, Eswar N, Penczek PA, Sali A, Blobel G, Frank J 
    (2001)
    Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions.
    Cell, 107(3), 373-86  (Details) (Pub Med ID: 11701127)
    Times cited: 317
    


89. Beckmann R, Spahn CM, Eswar N, Helmers J, Penczek PA, Sali A, Frank J, Blobel G 
    (2001)
    Architecture of the protein-conducting channel associated with the translating 80S ribosome.
    Cell, 107(3), 361-72  (Details) (Pub Med ID: 11701126)
    Times cited: 241
    


90. Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M 
    (2001)
    A functional update of the Escherichia coli K-12 genome.
    Genome Biology, 2(9), RESEARCH0035  (Details) (Pub Med ID: 11574054)
    Times cited: 4
    


91. Marti-Renom MA, Ilyin VA, Sali A 
    (2001)
    DBAli: a database of protein structure alignments.
    Bioinformatics, 17(8), 746-7  (Details) (Pub Med ID: 11524379)
    Times cited: 31
    


92. Gaasterland T, Oprea M 
    (2001)
    Whole-genome analysis: annotations and updates.
    Current Opinion in Structural Biology, 11(3), 377-81  (Details) (Pub Med ID: 11406390)
    Times cited: 24
    


93. Sali A 
    (2001)
    Target practice.
    Nature Structural & Molecular Biology, 8(6), 482-4  (Details) (Pub Med ID: 11373610)
    Times cited: 20
    


94. Gopal S, Schroeder M, Pieper U, Sczyrba A, Aytekin-Kurban G, Bekiranov S, Fajardo JE, Eswar N, Sanchez R, Sali A, Gaasterland T 
    (2001)
    Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome.
    Nature Genetics, 27(3), 337-40  (Details) (Pub Med ID: 11242120)
    Times cited: 45
    



2000 (click to unfold)

95. Sánchez R, Pieper U, Melo F, Eswar N, Martí-Renom MA, Madhusudhan MS, Mirković N, Sali A 
    (2000)
    Protein structure modeling for structural genomics.
    Nature Structural & Molecular Biology, 7 Suppl(41), 986-90  (Details) (Pub Med ID: 11104007)
    Times cited: 131
    


96. Burley SK 
    (2000)
    An overview of structural genomics.
    Nature Structural & Molecular Biology, 7 Suppl(5), 932-4  (Details) (Pub Med ID: 11103991)
    Times cited: 158
    


97. Jin S, Martinek S, Joo WS, Wortman JR, Mirkovic N, Sali A, Yandell MD, Pavletich NP, Young MW, Levine AJ 
    (2000)
    Identification and characterization of a p53 homologue in Drosophila melanogaster.
    Proceedings of the National Academy of Sciences of the United States of America, 97(13), 7301-6  (Details) (Pub Med ID: 10860994)
    Times cited: 123
    

Total number of citations for methodological publications: 5840
Average number of citations per publication (methodological): 60.2

(default) 37 queries took 148 ms

Nr	Query	Error	Affected	Num. rows	Took (ms)
1	SELECT table_name as name FROM INFORMATION_SCHEMA.tables WHERE table_schema = 'public';		0	21	8
2	SELECT DISTINCT column_name AS name, data_type AS type, is_nullable AS null, column_default AS default, ordinal_position AS position, character_maximum_length AS char_length, character_octet_length AS oct_length FROM information_schema.columns WHERE table_name = 'publication' AND (table_schema = 'public') ORDER BY position		0	29	13
3	SELECT DISTINCT column_name AS name, data_type AS type, is_nullable AS null, column_default AS default, ordinal_position AS position, character_maximum_length AS char_length, character_octet_length AS oct_length FROM information_schema.columns WHERE table_name = 'journal_alias' AND (table_schema = 'public') ORDER BY position		0	2	6
4	SELECT DISTINCT column_name AS name, data_type AS type, is_nullable AS null, column_default AS default, ordinal_position AS position, character_maximum_length AS char_length, character_octet_length AS oct_length FROM information_schema.columns WHERE table_name = 'journal' AND (table_schema = 'public') ORDER BY position		0	6	7
5	SELECT DISTINCT column_name AS name, data_type AS type, is_nullable AS null, column_default AS default, ordinal_position AS position, character_maximum_length AS char_length, character_octet_length AS oct_length FROM information_schema.columns WHERE table_name = 'initiative' AND (table_schema = 'public') ORDER BY position		0	3	7
6	SELECT DISTINCT column_name AS name, data_type AS type, is_nullable AS null, column_default AS default, ordinal_position AS position, character_maximum_length AS char_length, character_octet_length AS oct_length FROM information_schema.columns WHERE table_name = 'abstract' AND (table_schema = 'public') ORDER BY position		0	3	6
7	SELECT DISTINCT column_name AS name, data_type AS type, is_nullable AS null, column_default AS default, ordinal_position AS position, character_maximum_length AS char_length, character_octet_length AS oct_length FROM information_schema.columns WHERE table_name = 'publication_pdb' AND (table_schema = 'public') ORDER BY position		0	3	7
8	SELECT DISTINCT column_name AS name, data_type AS type, is_nullable AS null, column_default AS default, ordinal_position AS position, character_maximum_length AS char_length, character_octet_length AS oct_length FROM information_schema.columns WHERE table_name = 'technology' AND (table_schema = 'public') ORDER BY position		0	4	7
9	SELECT DISTINCT column_name AS name, data_type AS type, is_nullable AS null, column_default AS default, ordinal_position AS position, character_maximum_length AS char_length, character_octet_length AS oct_length FROM information_schema.columns WHERE table_name = 'publication_technology' AND (table_schema = 'public') ORDER BY position		0	3	6
10	SELECT DISTINCT column_name AS name, data_type AS type, is_nullable AS null, column_default AS default, ordinal_position AS position, character_maximum_length AS char_length, character_octet_length AS oct_length FROM information_schema.columns WHERE table_name = 'centers' AND (table_schema = 'public') ORDER BY position		0	12	8
11	SELECT DISTINCT "Center"."category" AS "Center__category" FROM "centers" AS "Center" WHERE "Center"."psi3" = TRUE		0	5	1
12	SELECT "Center"."id" AS "Center__id", "Center"."full_name" AS "Center__full_name" FROM "centers" AS "Center" WHERE "Center"."psi3" = TRUE AND "Center"."category" IS NULL ORDER BY "id" ASC		0	1	1
13	SELECT "Center"."id" AS "Center__id", "Center"."full_name" AS "Center__full_name" FROM "centers" AS "Center" WHERE "Center"."psi3" = TRUE AND "Center"."category" = 'resource' ORDER BY "id" ASC		0	2	1
14	SELECT "Center"."id" AS "Center__id", "Center"."full_name" AS "Center__full_name" FROM "centers" AS "Center" WHERE "Center"."psi3" = TRUE AND "Center"."category" = 'membrane' ORDER BY "id" ASC		0	9	0
15	SELECT "Center"."id" AS "Center__id", "Center"."full_name" AS "Center__full_name" FROM "centers" AS "Center" WHERE "Center"."psi3" = TRUE AND "Center"."category" = 'biology' ORDER BY "id" ASC		0	12	0
16	SELECT "Center"."id" AS "Center__id", "Center"."full_name" AS "Center__full_name" FROM "centers" AS "Center" WHERE "Center"."psi3" = TRUE AND "Center"."category" = 'ht' ORDER BY "id" ASC		0	4	0
17	SELECT "Center"."id" AS "Center__id", "Center"."full_name" AS "Center__full_name" FROM "centers" AS "Center" WHERE (("Center"."psi1" = TRUE) OR ("Center"."psi2" = TRUE)) ORDER BY "id" ASC		0	18	1
18	SELECT "Center"."id" AS "Center__id" FROM "centers" AS "Center" WHERE "nih" = TRUE AND (("Center"."psi1" = TRUE) OR ("Center"."psi2" = TRUE) OR ("Center"."psi3" = TRUE)) ORDER BY "id" ASC		0	38	1
19	SELECT COUNT(*), SUM(times_cited) FROM publication WHERE true AND (status = 'published' AND ((verified = 't' AND (source = 'spreadsheet' OR source = 'mcsg database' OR source = 'email')) OR source = 'psi_interface')) AND (center like '%ATCG3D%' OR center like '%BSGC%' OR center like '%CEBS%' OR center like '%CELLMAT%' OR center like '%CESG%' OR center like '%CHSAM%' OR center like '%CHTSB%' OR center like '%CSMP%' OR center like '%GPCR%' OR center like '%IFN%' OR center like '%ISFI%' OR center like '%JCMM%' OR center like '%JCSG%' OR center like '%MCSG%' OR center like '%MPID%' OR center like '%MPP%' OR center like '%MPSBC%' OR center like '%MPSbyNMR%' OR center like '%MTBI%' OR center like '%NatPro%' OR center like '%NESG%' OR center like '%NMHRCM%' OR center like '%NPCXstals%' OR center like '%NYCOMPS%' OR center like '%NYSGRC%' OR center like '%NYSGXRC%' OR center like '%PCSEP%' OR center like '%PSIMR%' OR center like '%PSISBKB%' OR center like '%SECSG%' OR center like '%SGPP%' OR center like '%STEMCELL%' OR center like '%TB%' OR center like '%TCELL%' OR center like '%TEMIMPS%' OR center like '%TJMP%' OR center like '%TMPC%' OR center like '%TransportPDB%')		0	1	9
20	SELECT COUNT(*), SUM(times_cited) FROM publication WHERE (type='method' OR type='other') AND (status = 'published' AND ((verified = 't' AND (source = 'spreadsheet' OR source = 'mcsg database' OR source = 'email')) OR source = 'psi_interface')) AND (center like '%ATCG3D%' OR center like '%BSGC%' OR center like '%CEBS%' OR center like '%CELLMAT%' OR center like '%CESG%' OR center like '%CHSAM%' OR center like '%CHTSB%' OR center like '%CSMP%' OR center like '%GPCR%' OR center like '%IFN%' OR center like '%ISFI%' OR center like '%JCMM%' OR center like '%JCSG%' OR center like '%MCSG%' OR center like '%MPID%' OR center like '%MPP%' OR center like '%MPSBC%' OR center like '%MPSbyNMR%' OR center like '%MTBI%' OR center like '%NatPro%' OR center like '%NESG%' OR center like '%NMHRCM%' OR center like '%NPCXstals%' OR center like '%NYCOMPS%' OR center like '%NYSGRC%' OR center like '%NYSGXRC%' OR center like '%PCSEP%' OR center like '%PSIMR%' OR center like '%PSISBKB%' OR center like '%SECSG%' OR center like '%SGPP%' OR center like '%STEMCELL%' OR center like '%TB%' OR center like '%TCELL%' OR center like '%TEMIMPS%' OR center like '%TJMP%' OR center like '%TMPC%' OR center like '%TransportPDB%')		0	1	5
21	SELECT COUNT(*), SUM(times_cited) FROM publication WHERE (type='structure' OR type='note' OR type='function') AND (status = 'published' AND ((verified = 't' AND (source = 'spreadsheet' OR source = 'mcsg database' OR source = 'email')) OR source = 'psi_interface')) AND (center like '%ATCG3D%' OR center like '%BSGC%' OR center like '%CEBS%' OR center like '%CELLMAT%' OR center like '%CESG%' OR center like '%CHSAM%' OR center like '%CHTSB%' OR center like '%CSMP%' OR center like '%GPCR%' OR center like '%IFN%' OR center like '%ISFI%' OR center like '%JCMM%' OR center like '%JCSG%' OR center like '%MCSG%' OR center like '%MPID%' OR center like '%MPP%' OR center like '%MPSBC%' OR center like '%MPSbyNMR%' OR center like '%MTBI%' OR center like '%NatPro%' OR center like '%NESG%' OR center like '%NMHRCM%' OR center like '%NPCXstals%' OR center like '%NYCOMPS%' OR center like '%NYSGRC%' OR center like '%NYSGXRC%' OR center like '%PCSEP%' OR center like '%PSIMR%' OR center like '%PSISBKB%' OR center like '%SECSG%' OR center like '%SGPP%' OR center like '%STEMCELL%' OR center like '%TB%' OR center like '%TCELL%' OR center like '%TEMIMPS%' OR center like '%TJMP%' OR center like '%TMPC%' OR center like '%TransportPDB%')		0	1	3
22	SELECT SUM(impact_factor) as impact FROM publication, journal, journal_alias WHERE journal_short = name AND journal.id = journal_id AND true AND (status = 'published' AND ((verified = 't' AND (source = 'spreadsheet' OR source = 'mcsg database' OR source = 'email')) OR source = 'psi_interface')) AND (center like '%ATCG3D%' OR center like '%BSGC%' OR center like '%CEBS%' OR center like '%CELLMAT%' OR center like '%CESG%' OR center like '%CHSAM%' OR center like '%CHTSB%' OR center like '%CSMP%' OR center like '%GPCR%' OR center like '%IFN%' OR center like '%ISFI%' OR center like '%JCMM%' OR center like '%JCSG%' OR center like '%MCSG%' OR center like '%MPID%' OR center like '%MPP%' OR center like '%MPSBC%' OR center like '%MPSbyNMR%' OR center like '%MTBI%' OR center like '%NatPro%' OR center like '%NESG%' OR center like '%NMHRCM%' OR center like '%NPCXstals%' OR center like '%NYCOMPS%' OR center like '%NYSGRC%' OR center like '%NYSGXRC%' OR center like '%PCSEP%' OR center like '%PSIMR%' OR center like '%PSISBKB%' OR center like '%SECSG%' OR center like '%SGPP%' OR center like '%STEMCELL%' OR center like '%TB%' OR center like '%TCELL%' OR center like '%TEMIMPS%' OR center like '%TJMP%' OR center like '%TMPC%' OR center like '%TransportPDB%')		0	1	7
23	SELECT count(*) FROM publication WHERE times_cited>=5 AND true AND (status = 'published' AND ((verified = 't' AND (source = 'spreadsheet' OR source = 'mcsg database' OR source = 'email')) OR source = 'psi_interface')) AND (center like '%ATCG3D%' OR center like '%BSGC%' OR center like '%CEBS%' OR center like '%CELLMAT%' OR center like '%CESG%' OR center like '%CHSAM%' OR center like '%CHTSB%' OR center like '%CSMP%' OR center like '%GPCR%' OR center like '%IFN%' OR center like '%ISFI%' OR center like '%JCMM%' OR center like '%JCSG%' OR center like '%MCSG%' OR center like '%MPID%' OR center like '%MPP%' OR center like '%MPSBC%' OR center like '%MPSbyNMR%' OR center like '%MTBI%' OR center like '%NatPro%' OR center like '%NESG%' OR center like '%NMHRCM%' OR center like '%NPCXstals%' OR center like '%NYCOMPS%' OR center like '%NYSGRC%' OR center like '%NYSGXRC%' OR center like '%PCSEP%' OR center like '%PSIMR%' OR center like '%PSISBKB%' OR center like '%SECSG%' OR center like '%SGPP%' OR center like '%STEMCELL%' OR center like '%TB%' OR center like '%TCELL%' OR center like '%TEMIMPS%' OR center like '%TJMP%' OR center like '%TMPC%' OR center like '%TransportPDB%')		0	1	4
24	SELECT "Center"."id" AS "Center__id", "Center"."full_name" AS "Center__full_name" FROM "centers" AS "Center" WHERE "nih" = TRUE AND (("psi1" = TRUE) OR ("psi2" = TRUE) OR ("psi3" = TRUE)) ORDER BY "id" ASC		0	38	1
25	SELECT "Center"."id" AS "Center__id", "Center"."full_name" AS "Center__full_name" FROM "centers" AS "Center" WHERE "nih" = TRUE AND (("psi1" = TRUE) OR ("psi2" = TRUE) OR ("psi3" = TRUE)) ORDER BY "id" ASC		0	38	1
26	SELECT COUNT(*), SUM(times_cited) FROM publication WHERE true AND (status = 'published' AND ((verified = 't' AND (source = 'spreadsheet' OR source = 'mcsg database' OR source = 'email')) OR source = 'psi_interface')) AND (center like '%NYSGRC%' or center like '%NYSGXRC%')		0	1	2
27	SELECT COUNT(*), SUM(times_cited) FROM publication WHERE (type='method' OR type='other') AND (status = 'published' AND ((verified = 't' AND (source = 'spreadsheet' OR source = 'mcsg database' OR source = 'email')) OR source = 'psi_interface')) AND (center like '%NYSGRC%' or center like '%NYSGXRC%')		0	1	1
28	SELECT COUNT(*), SUM(times_cited) FROM publication WHERE (type='structure' OR type='note' OR type='function') AND (status = 'published' AND ((verified = 't' AND (source = 'spreadsheet' OR source = 'mcsg database' OR source = 'email')) OR source = 'psi_interface')) AND (center like '%NYSGRC%' or center like '%NYSGXRC%')		0	1	2
29	SELECT SUM(impact_factor) as impact FROM publication, journal, journal_alias WHERE journal_short = name AND journal.id = journal_id AND true AND (status = 'published' AND ((verified = 't' AND (source = 'spreadsheet' OR source = 'mcsg database' OR source = 'email')) OR source = 'psi_interface')) AND (center like '%NYSGRC%' or center like '%NYSGXRC%')		0	1	2
30	SELECT count(*) FROM publication WHERE times_cited>=5 AND true AND (status = 'published' AND ((verified = 't' AND (source = 'spreadsheet' OR source = 'mcsg database' OR source = 'email')) OR source = 'psi_interface')) AND (center like '%NYSGRC%' or center like '%NYSGXRC%')		0	1	1
31	SELECT year, type, count(*) FROM publication WHERE (status = 'published' AND ((verified = 't' AND (source = 'spreadsheet' OR source = 'mcsg database' OR source = 'email')) OR source = 'psi_interface')) AND (center like '%NYSGRC%' or center like '%NYSGXRC%') GROUP BY year, type ORDER BY year DESC		0	36	3
32	SELECT year, count(*) FROM publication WHERE (type='structure' OR type='note' OR type='function') AND (status = 'published' AND ((verified = 't' AND (source = 'spreadsheet' OR source = 'mcsg database' OR source = 'email')) OR source = 'psi_interface')) AND (center like '%NYSGRC%' or center like '%NYSGXRC%') GROUP BY year ORDER BY year DESC		0	12	3
33	SELECT year, count(*) FROM publication WHERE (type='method' OR type='other') AND (status = 'published' AND ((verified = 't' AND (source = 'spreadsheet' OR source = 'mcsg database' OR source = 'email')) OR source = 'psi_interface')) AND (center like '%NYSGRC%' or center like '%NYSGXRC%') GROUP BY year ORDER BY year DESC		0	12	2
34	SELECT "Publication"."id" AS "Publication__id","Publication"."pmid" AS "Publication__pmid","Publication"."authors" AS "Publication__authors","Publication"."title" AS "Publication__title","Publication"."journal_short" AS "Publication__journal_short","Publication"."issn" AS "Publication__issn","Publication"."year" AS "Publication__year","Publication"."vol" AS "Publication__vol","Publication"."pages" AS "Publication__pages","Publication"."center" AS "Publication__center","Publication"."target_id" AS "Publication__target_id","Publication"."pdb_id" AS "Publication__pdb_id","Publication"."type" AS "Publication__type","Publication"."status" AS "Publication__status","Publication"."source" AS "Publication__source","Publication"."remark" AS "Publication__remark","Publication"."verified" AS "Publication__verified","Publication"."frozen" AS "Publication__frozen","Publication"."times_cited" AS "Publication__times_cited","Publication"."times_cited_update" AS "Publication__times_cited_update","Publication"."inserted" AS "Publication__inserted","Publication"."updated" AS "Publication__updated","Publication"."times_cited_status" AS "Publication__times_cited_status","Publication"."pubmed_times_cited" AS "Publication__pubmed_times_cited","Publication"."pubmed_times_cited_update" AS "Publication__pubmed_times_cited_update","Publication"."pubmed_times_cited_status" AS "Publication__pubmed_times_cited_status","Publication"."cover_image" AS "Publication__cover_image","Publication"."initiative_id" AS "Publication__initiative_id","Publication"."pmcid" AS "Publication__pmcid","Journal"."id" as "Journal__id","Journal"."display_name" as "Journal__display_name","PubAbstract"."abstract" as "PubAbstract__abstract","Initiative"."name" as "Initiative__name","Initiative"."short_name" as "Initiative__short_name" FROM publication as "Publication" LEFT JOIN journal_alias as "JournalAlias" on "Publication".journal_short = "JournalAlias".name LEFT JOIN journal as "Journal" on "JournalAlias".journal_id = "Journal".id LEFT JOIN initiative as "Initiative" on "Publication".initiative_id = "Initiative".id LEFT JOIN abstract as "PubAbstract" on "PubAbstract".publication_id = "Publication".id WHERE (status = 'published' AND ((verified = 't' AND (source = 'spreadsheet' OR source = 'mcsg database' OR source = 'email')) OR source = 'psi_interface')) AND (((type='structure' OR type='note' OR type='function')) AND ((center like '%NYSGRC%' or center like '%NYSGXRC%'))) ORDER BY "year" DESC, "pmid" DESC, "status" ASC		0	87	10
35	SELECT "PublicationPdb"."id" AS "PublicationPdb__id", "PublicationPdb"."publication_id" AS "PublicationPdb__publication_id", "PublicationPdb"."pdb_id" AS "PublicationPdb__pdb_id" FROM "publication_pdb" AS "PublicationPdb" WHERE 1 = 1		0	1175	2
36	SELECT "Publication"."id" AS "Publication__id","Publication"."pmid" AS "Publication__pmid","Publication"."authors" AS "Publication__authors","Publication"."title" AS "Publication__title","Publication"."journal_short" AS "Publication__journal_short","Publication"."issn" AS "Publication__issn","Publication"."year" AS "Publication__year","Publication"."vol" AS "Publication__vol","Publication"."pages" AS "Publication__pages","Publication"."center" AS "Publication__center","Publication"."target_id" AS "Publication__target_id","Publication"."pdb_id" AS "Publication__pdb_id","Publication"."type" AS "Publication__type","Publication"."status" AS "Publication__status","Publication"."source" AS "Publication__source","Publication"."remark" AS "Publication__remark","Publication"."verified" AS "Publication__verified","Publication"."frozen" AS "Publication__frozen","Publication"."times_cited" AS "Publication__times_cited","Publication"."times_cited_update" AS "Publication__times_cited_update","Publication"."inserted" AS "Publication__inserted","Publication"."updated" AS "Publication__updated","Publication"."times_cited_status" AS "Publication__times_cited_status","Publication"."pubmed_times_cited" AS "Publication__pubmed_times_cited","Publication"."pubmed_times_cited_update" AS "Publication__pubmed_times_cited_update","Publication"."pubmed_times_cited_status" AS "Publication__pubmed_times_cited_status","Publication"."cover_image" AS "Publication__cover_image","Publication"."initiative_id" AS "Publication__initiative_id","Publication"."pmcid" AS "Publication__pmcid","Journal"."id" as "Journal__id","Journal"."display_name" as "Journal__display_name","PubAbstract"."abstract" as "PubAbstract__abstract","Initiative"."name" as "Initiative__name","Initiative"."short_name" as "Initiative__short_name" FROM publication as "Publication" LEFT JOIN journal_alias as "JournalAlias" on "Publication".journal_short = "JournalAlias".name LEFT JOIN journal as "Journal" on "JournalAlias".journal_id = "Journal".id LEFT JOIN initiative as "Initiative" on "Publication".initiative_id = "Initiative".id LEFT JOIN abstract as "PubAbstract" on "PubAbstract".publication_id = "Publication".id WHERE (status = 'published' AND ((verified = 't' AND (source = 'spreadsheet' OR source = 'mcsg database' OR source = 'email')) OR source = 'psi_interface')) AND (((type='method' OR type='other')) AND ((center like '%NYSGRC%' or center like '%NYSGXRC%'))) ORDER BY "year" DESC, "pmid" DESC, "status" ASC		0	97	8
37	SELECT "PublicationPdb"."id" AS "PublicationPdb__id", "PublicationPdb"."publication_id" AS "PublicationPdb__publication_id", "PublicationPdb"."pdb_id" AS "PublicationPdb__pdb_id" FROM "publication_pdb" AS "PublicationPdb" WHERE 1 = 1		0	1175	2