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Publications for New York Structural Genomics Research Consortium
| Total Publications | 181 |
|---|---|
| Publications with >5 Citations | 141 |
| Structural Publications | 86 |
| Methodological and Other Publications | 95 |
| Total Citations | 7885 |
| Avg. Citations (Structural) | 22.1 |
| Avg. Citations (Methodological and Other) | 63.0 |
| Total Impact | 1,145.7 |
More New York Structural Genomics Research Consortium statistics here.
Structural Publications
- Structural basis for a ribofuranosyl binding protein: Insights into the furanose specific transport.
Bagaria A, Kumaran D, Burley SK, Swaminathan S
Proteins (2011) , 79, 1352-7
(Details) (Pub Med ID: 21387413)
Target: NYSGXRC-11023l
PDB ID(s): 3KSM
Times cited: 0 - Enzymatic deamination of the epigenetic base N-6-methyladenine.
Kamat SS, Fan H, Sauder JM, Burley SK, Shoichet BK, Sali A, Raushel FM
Journal of the American Chemical Society (2011) , 133, 2080-3
(Details) (Pub Med ID: 21275375)
Target: NYSGXRC-9208a
Times cited: no data - Catalytic mechanism and three-dimensional structure of adenine deaminase.
Kamat SS, Bagaria A, Kumaran D, Holmes-Hampton GP, Fan H, Sali A, Sauder JM, Burley SK, Lindahl PA, Swaminathan S, Raushel FM
Biochemistry (2011) , 50, 1917-27
(Details) (Pub Med ID: 21247091)
Target: NYSGXRC-9206aTimes cited: 4 - Structural and functional studies of fatty acyl adenylate ligases from E. coli and L. pneumophila.
Zhang Z, Zhou R, Sauder JM, Tonge PJ, Burley SK, Swaminathan S
Journal of Molecular Biology (2011) , 406, 313-24
(Details) (Pub Med ID: 21185305)
Target: NYSGXRC-11191gTimes cited: 1 - Structural underpinnings of nitrogen regulation by the prototypical nitrogen-responsive transcriptional factor NrpR.
Wisedchaisri G, Dranow DM, Lie TJ, Bonanno JB, Patskovsky Y, Ozyurt SA, Sauder JM, Almo SC, Wasserman SR, Burley SK, Leigh JA, Gonen T
Structure (2010) , 18, 1512-21
(Details) (Pub Med ID: 21070950)
Target: NYSGXRC-10196a
PDB ID(s): 3NEKTimes cited: 1 - Structural bases of PAS domain-regulated kinase (PASK) activation in the absence of activation loop phosphorylation.
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
Journal of Biological Chemistry (2010) , 285, 41034-43
(Details) (Pub Med ID: 20943661)
Target: NYSGXRC-9501a
PDB ID(s): 3DLSTimes cited: 3 - Structure of a putative BenF-like porin from Pseudomonas fluorescens Pf-5 at 2.6 A resolution.
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
Proteins (2010) , 78, 3056-62
(Details) (Pub Med ID: 20737437)
Target: NYSGXRC-10383p
PDB ID(s): 3JTYTimes cited: 4 - Functional identification and structure determination of two novel prolidases from cog1228 in the amidohydrolase superfamily .
Xiang DF, Patskovsky Y, Xu C, Fedorov AA, Fedorov EV, Sisco AA, Sauder JM, Burley SK, Almo SC, Raushel FM
Biochemistry (2010) , 49, 6791-803
(Details) (Pub Med ID: 20604542)
Target: 9260c
PDB ID(s): 3MKV 3FEQ 3N2CTimes cited: 3 - Discovery and Structure Determination of the Orphan Enzyme Isoxanthopterin Deaminase .
Hall RS, Agarwal R, Hitchcock D, Sauder JM, Burley SK, Swaminathan S, Raushel FM
Biochemistry (2010) , 49, 4374-82
(Details) (Pub Med ID: 20415463)
Target: NYSGXRC-9339a
PDB ID(s): 2PAJTimes cited: 5 - Structures of the autoproteolytic domain from the Saccharomyces cerevisiae nuclear pore complex component, Nup145.
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
Proteins (2010) , 78, 1992-8
(Details) (Pub Med ID: 20310066)
Target: NYSGXRC-15145a
PDB ID(s): 3KEP 3KESTimes cited: 3 - Structures of PHR Domains from Mus musculus Phr1 (Mycbp2) Explain the Loss-of-Function Mutation (Gly1092-->Glu) of the C. elegans Ortholog RPM-1.
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
Journal of Molecular Biology (2010) , 397, 883-92
(Details) (Pub Med ID: 20156452)
Target: NYSGXRC-13170b
PDB ID(s): 3GBW 3HWJ
Times cited: 0 - The hunt for 8-oxoguanine deaminase.
Hall RS, Fedorov AA, Marti-Arbona R, Fedorov EV, Kolb P, Sauder JM, Burley SK, Shoichet BK, Almo SC, Raushel FM
Accounts of Chemical Research (2010) , 132, 1762-3
(Details) (Pub Med ID: 20088583)
Target: NYSGXRC-9236e
PDB ID(s): 3H4UTimes cited: 8 - Structure of YqgQ protein from Bacillus subtilis, a conserved hypothetical protein.
Lakshminarasimhan D, Eswaramoorthy S, Burley SK, Swaminathan S
Acta Crystallographica Section F: Structural Biology and Crystallization Communications (2010) , 66, 8-11
(Details) (Pub Med ID: 20057058)
Target: NYSGXRC-10278a
PDB ID(s): 2NN4
Times cited: 0 - Computation-Facilitated Assignment of the Function in the Enolase Superfamily: A Regiochemically Distinct Galactarate Dehydratase from Oceanobacillus iheyensis .
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
Biochemistry (2009) , 48, 11546-58
(Details) (Pub Med ID: 19883118)
Target: NYSGXRC-9375a
PDB ID(s): 2OQYTimes cited: 7 - Periplasmic domains of Pseudomonas aeruginosa PilN and PilO form a stable heterodimeric complex.
Sampaleanu LM, Bonanno JB, Ayers M, Koo J, Tammam S, Burley SK, Almo SC, Burrows LL, Howell PL
Journal of Molecular Biology (2009) , 394, 143-59
(Details) (Pub Med ID: 19857646)
Target: NYSGXRC-10146c
PDB ID(s): 2RJZTimes cited: 11 - Crystal structure of native RPE65, the retinoid isomerase of the visual cycle.
Kiser PD, Golczak M, Lodowski DT, Chance MR, Palczewski K
Proceedings of the National Academy of Sciences of the United States of America (2009) , 106, 17325-30
(Details) (Pub Med ID: 19805034)
Target: NYSGXRC-9507a
PDB ID(s): 3FSNTimes cited: 25 - Structural studies on cytosolic domain of magnesium transporter MgtE from Enterococcus faecalis.
Ragumani S, Sauder JM, Burley SK, Swaminathan S
Proteins (2009) , 78, 487-91
(Details) (Pub Med ID: 19787770)
Target: NYSGXRC-10001b
PDB ID(s): 2OUX
Times cited: no data - Structure of a microsporidian methionine aminopeptidase type 2 complexed with fumagillin and TNP-470.
Alvarado JJ, Nemkal A, Sauder JM, Russell M, Akiyoshi DE, Shi W, Almo SC, Weiss LM
Molecular and Biochemical Parasitology (2009) , 168, 158-67
(Details) (Pub Med ID: 19660503)
Target: NYSGXRC-9201a
PDB ID(s): 3FM3 3FMQ 3FMRTimes cited: 3 - Functional Annotation of Two New Carboxypeptidases from the Amidohydrolase Superfamily of Enzymes.
Xiang DF, Xu C, Kumaran D, Brown AC, Sauder JM, Burley SK, Swaminathan S, Raushel FM
Biochemistry (2009) , 48, 4567-76
(Details) (Pub Med ID: 19358546)
PDB ID(s): 2QS8Times cited: 6 - Functional identification of incorrectly annotated prolidases from the amidohydrolase superfamily of enzymes.
Xiang DF, Patskovsky Y, Xu C, Meyer AJ, Sauder JM, Burley SK, Almo SC, Raushel FM
Biochemistry (2009) , 48, 3730-42
(Details) (Pub Med ID: 19281183)
PDB ID(s): 3BE7 3DUGTimes cited: 7 - Type VI secretion apparatus and phage tail-associated protein complexes share a common evolutionary origin.
Leiman PG, Basler M, Ramagopal UA, Bonanno JB, Sauder JM, Pukatzki S, Burley SK, Almo SC, Mekalanos JJ
Proceedings of the National Academy of Sciences of the United States of America (2009) , 106, 4154-9
(Details) (Pub Med ID: 19251641)
PDB ID(s): 2P5ZTimes cited: 68 - Evolution of enzymatic activities in the enolase superfamily: stereochemically distinct mechanisms in two families of cis,cis-muconate lactonizing enzymes.
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
Biochemistry (2009) , 48, 1445-53
(Details) (Pub Med ID: 19220063)
PDB ID(s): 3DG3 3DG6 3DG7 3DGB 3CT2Times cited: 7 - UPF201 archaeal specific family members reveal structural similarity to RNA-binding proteins but low likelihood for RNA-binding function.
Rao KN, Burley SK, Swaminathan S
PLoS ONE (2008) , 3, e3903
(Details) (Pub Med ID: 19079550)
PDB ID(s): 2PZZ 2NRQ 2NWU 2OGK
Times cited: 0 - Structural characterization and reversal of the natural organophosphate resistance of a D-type esterase, Saccharomyces cerevisiae S-formylglutathione hydrolase.
Legler PM, Kumaran D, Swaminathan S, Studier FW, Millard CB
Biochemistry (2008) , 47, 9592-601
(Details) (Pub Med ID: 18707125)
PDB ID(s): 1PV1Times cited: 7 - Crystal structure of a putative lysostaphin peptidase from Vibrio cholerae.
Ragumani S, Kumaran D, Burley SK, Swaminathan S
Proteins (2008) , 72, 1096-103
(Details) (Pub Med ID: 18498110)
PDB ID(s): 2GU1Times cited: 4 - A common catalytic mechanism for proteins of the HutI family.
Tyagi R, Eswaramoorthy S, Burley SK, Raushel FM, Swaminathan S
Biochemistry (2008) , 47(20), 5608-15
(Details) (Pub Med ID: 18442260)
PDB ID(s): 2Q09Times cited: 3 - A novel mode of dimerization via formation of a glutamate anhydride crosslink in a protein crystal structure.
Agarwal R, Burley SK, Swaminathan S
Proteins (2008) , 71(2), 1038-41
(Details) (Pub Med ID: 18247349)
PDB ID(s): 1SG9
Times cited: 0 - Structure of human dual specificity protein phosphatase 23, VHZ, enzyme-substrate/product complex.
Agarwal R, Burley SK, Swaminathan S
Journal of Biological Chemistry (2008) , 283(14), 8946-53
(Details) (Pub Med ID: 18245086)
PDB ID(s): 2IMGTimes cited: 7 - X-ray crystal structure of the B component of Hemolysin BL from Bacillus cereus.
Madegowda M, Eswaramoorthy S, Burley SK, Swaminathan S
Proteins (2008) , 71, 534-40
(Details) (Pub Med ID: 18175317)
PDB ID(s): 2NRJTimes cited: 5 - Crystal structure of a conserved protein of unknown function (MJ1651) from Methanococcus jannaschii.
Rao KN, Burley SK, Swaminathan S
Proteins (2008) , 70(2), 572-7
(Details) (Pub Med ID: 17910070)
PDB ID(s): 2F4NTimes cited: 1 - Structural genomics of protein phosphatases.
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
Journal of Structural and Functional Genomics (2007) , 8(2-3), 121-40
(Details) (Pub Med ID: 18058037)
PDB ID(s): 2FH7Times cited: 27 - X-ray structures of two proteins belonging to Pfam DUF178 revealed unexpected structural similarity to the DUF191 Pfam family.
Tyagi R, Burley SK, Swaminathan S
BMC Structural Biology (2007) , 7(6), 62
(Details) (Pub Med ID: 17908300)
PDB ID(s): 2I6ETimes cited: 1 - X-ray structure of imidazolonepropionase from Agrobacterium tumefaciens at 1.87 A resolution.
Tyagi R, Kumaran D, Burley SK, Swaminathan S
Proteins (2007) , 69(3), 652-8
(Details) (Pub Med ID: 17640072)
PDB ID(s): 2PUZTimes cited: 2 - Structure-based activity prediction for an enzyme of unknown function.
Hermann JC, Marti-Arbona R, Fedorov AA, Fedorov E, Almo SC, Shoichet BK, Raushel FM
Nature (2007) , 448(7155), 775-9
(Details) (Pub Med ID: 17603473)
PDB ID(s): 2PLMTimes cited: 102 - 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.
Velge P, Herler M, Johansson J, Roche SM, Témoin S, Fedorov AA, Gracieux P, Almo SC, Goebel W, Cossart P
Microbiology (2007) , 153(Pt 4), 995-1005
(Details) (Pub Med ID: 17379709)
PDB ID(s): 1OMITimes cited: 15 - Structural analysis of a ternary complex of allantoate amidohydrolase from Escherichia coli reveals its mechanics.
Agarwal R, Burley SK, Swaminathan S
Journal of Molecular Biology (2007) , 368(2), 450-63
(Details) (Pub Med ID: 17362992)
PDB ID(s): 1Z2LTimes cited: 15 - Structural analysis of the plakin domain of bullous pemphigoid antigen1 (BPAG1) suggests that plakins are members of the spectrin superfamily.
Jefferson JJ, Ciatto C, Shapiro L, Liem RK
Journal of Molecular Biology (2007) , 366(1), 244-57
(Details) (Pub Med ID: 17161423)
PDB ID(s): 2IAKTimes cited: 18 - Crystal structure of glycerophosphodiester phosphodiesterase from Agrobacterium tumefaciens by SAD with a large asymmetric unit.
Rao KN, Bonanno JB, Burley SK, Swaminathan S
Proteins (2006) , 65(2), 514-8
(Details) (Pub Med ID: 16909422)
PDB ID(s): 1ZCCTimes cited: 7 - Crystal structure of phosphatidylglycerophosphatase (PGPase), a putative membrane-bound lipid phosphatase, reveals a novel binuclear metal binding site and two "proton wires".
Kumaran D, Bonanno JB, Burley SK, Swaminathan S
Proteins (2006) , 64(4), 851-62
(Details) (Pub Med ID: 16838328)
PDB ID(s): 1Y9ITimes cited: 3 - Crystal structure of trehalose-6-phosphate phosphatase-related protein: biochemical and biological implications.
Rao KN, Kumaran D, Seetharaman J, Bonanno JB, Burley SK, Swaminathan S
Protein Science (2006) , 15(7), 1735-44
(Details) (Pub Med ID: 16815921)
PDB ID(s): 1U02Times cited: 8 - Mechanism of action of a flavin-containing monooxygenase.
Eswaramoorthy S, Bonanno JB, Burley SK, Swaminathan S
Proceedings of the National Academy of Sciences of the United States of America (2006) , 103(26), 9832-7
(Details) (Pub Med ID: 16777962)
PDB ID(s): 2GV8Times cited: 40 - Crystal structure of Escherichia coli L-arabinose isomerase (ECAI), the putative target of biological tagatose production.
Manjasetty BA, Chance MR
Journal of Molecular Biology (2006) , 360(2), 297-309
(Details) (Pub Med ID: 16756997)
PDB ID(s): 2AJTTimes cited: 26 - Structure determination of an FMN reductase from Pseudomonas aeruginosa PA01 using sulfur anomalous signal.
Agarwal R, Bonanno JB, Burley SK, Swaminathan S
Acta Crystallographica Section D: Biological Crystallography (2006) , 62(Pt 4), 383-91
(Details) (Pub Med ID: 16552139)
PDB ID(s): 1RTTTimes cited: 19 - Crystal structures of two putative phosphoheptose isomerases.
Seetharaman J, Rajashankar KR, Solorzano V, Kniewel R, Lima CD, Bonanno JB, Burley SK, Swaminathan S
Proteins (2006) , 63(4), 1092-6
(Details) (Pub Med ID: 16477602)
PDB ID(s): 1TK9Times cited: 7 - Crystal structure of a putative HTH-type transcriptional regulator yxaF from Bacillus subtilis.
Seetharaman J, Kumaran D, Bonanno JB, Burley SK, Swaminathan S
Proteins (2006) , 63(4), 1087-91
(Details) (Pub Med ID: 16475182)
PDB ID(s): 1SGMTimes cited: 3 - Structure, function, and mechanism of the phenylacetate pathway hot dog-fold thioesterase PaaI.
Song F, Zhuang Z, Finci L, Dunaway-Mariano D, Kniewel R, Buglino JA, Solorzano V, Wu J, Lima CD
Journal of Biological Chemistry (2006) , 281(16), 11028-38
(Details) (Pub Med ID: 16464851)
PDB ID(s): 2FS2Times cited: 22 - Structures of wild-type and mutant human spermidine/spermine N1-acetyltransferase, a potential therapeutic drug target.
Bewley MC, Graziano V, Jiang J, Matz E, Studier FW, Pegg AE, Coleman CS, Flanagan JM
Proceedings of the National Academy of Sciences of the United States of America (2006) , 103(7), 2063-8
(Details) (Pub Med ID: 16455797)
PDB ID(s): 2B3UTimes cited: 18 - The ybeY protein from Escherichia coli is a metalloprotein.
Zhan C, Fedorov EV, Shi W, Ramagopal UA, Thirumuruhan R, Manjasetty BA, Almo SC, Fiser A, Chance MR, Fedorov AA
Acta Crystallographica Section F: Structural Biology and Crystallization Communications (2005) , 61(Pt 11), 959-63
(Details) (Pub Med ID: 16511207)
PDB ID(s): 1XM5Times cited: 9 - Crystal structures of the tryptophan repressor binding protein WrbA and complexes with flavin mononucleotide.
Gorman J, Shapiro L
Protein Science (2005) , 14(12), 3004-12
(Details) (Pub Med ID: 16322580)
PDB ID(s): 1YRHTimes cited: 12 - Structural analysis of a set of proteins resulting from a bacterial genomics project.
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
Proteins (2005) , 60(4), 787-96
(Details) (Pub Med ID: 16021622)Times cited: 91 - Phased translation function revisited: structure solution of the cofilin-homology domain from yeast actin-binding protein 1 using six-dimensional searches.
Strokopytov BV, Fedorov A, Mahoney NM, Kessels M, Drubin DG, Almo SC
Acta Crystallographica Section D: Biological Crystallography (2005) , 61(Pt 3), 285-93
(Details) (Pub Med ID: 15735338)
PDB ID(s): 1HQZTimes cited: 14 - Structure and mechanism of ADP-ribose-1'-monophosphatase (Appr-1'-pase), a ubiquitous cellular processing enzyme.
Kumaran D, Eswaramoorthy S, Studier FW, Swaminathan S
Protein Science (2005) , 14(3), 719-26
(Details) (Pub Med ID: 15722447)
PDB ID(s): 1NJRTimes cited: 22 - X-ray structure of a Rex-family repressor/NADH complex insights into the mechanism of redox sensing.
Sickmier EA, Brekasis D, Paranawithana S, Bonanno JB, Paget MS, Burley SK, Kielkopf CL
Structure (2005) , 13(1), 43-54
(Details) (Pub Med ID: 15642260)
PDB ID(s): 1XCBTimes cited: 21 - Structure of serine acetyltransferase from Haemophilus influenzae Rd.
Gorman J, Shapiro L
Acta Crystallographica Section D: Biological Crystallography (2004) , 60(Pt 9), 1600-5
(Details) (Pub Med ID: 15333931)
PDB ID(s): 1S80Times cited: 14 - Crystal structure of the actin binding domain of the cyclase-associated protein.
Dodatko T, Fedorov AA, Grynberg M, Patskovsky Y, Rozwarski DA, Jaroszewski L, Aronoff-Spencer E, Kondraskina E, Irving T, Godzik A, Almo SC
Biochemistry (2004) , 43(33), 10628-41
(Details) (Pub Med ID: 15311924)Times cited: 18 - Disulfide-dependent multimeric assembly of resistin family hormones.
Patel SD, Rajala MW, Rossetti L, Scherer PE, Shapiro L
Science (2004) , 304(5674), 1154-8
(Details) (Pub Med ID: 15155948)
PDB ID(s): 1RH7Times cited: 117 - Identification of functional residues on Caenorhabditis elegans actin-interacting protein 1 (UNC-78) for disassembly of actin depolymerizing factor/cofilin-bound actin filaments.
Mohri K, Vorobiev S, Fedorov AA, Almo SC, Ono S
Journal of Biological Chemistry (2004) , 279(30), 31697-707
(Details) (Pub Med ID: 15150269)
PDB ID(s): 1NR0Times cited: 44 - Crystal structure of PapA5, a phthiocerol dimycocerosyl transferase from Mycobacterium tuberculosis.
Buglino J, Onwueme KC, Ferreras JA, Quadri LE, Lima CD
Journal of Biological Chemistry (2004) , 279(29), 30634-42
(Details) (Pub Med ID: 15123643)
PDB ID(s): 1Q9JTimes cited: 27 - Crystallization and preliminary crystallographic analysis of the Escherichia coli water channel AqpZ.
Daniels BV, Jiang JS, Fu D
Acta Crystallographica Section D: Biological Crystallography (2004) , 60(Pt 3), 561-3
(Details) (Pub Med ID: 14993693)Times cited: 5 - Structure of Escherichia coli YfdW, a type III CoA transferase.
Gogos A, Gorman J, Shapiro L
Acta Crystallographica Section D: Biological Crystallography (2004) , 60(Pt 3), 507-11
(Details) (Pub Med ID: 14993676)
PDB ID(s): 1Q7ETimes cited: 9 - Structure and mechanism of mRNA cap (guanine-N7) methyltransferase.
Fabrega C, Hausmann S, Shen V, Shuman S, Lima CD
Molecular Cell (2004) , 13(1), 77-89
(Details) (Pub Med ID: 14731396)
PDB ID(s): 1RI1Times cited: 60 - Structural bases for CRMP function in plexin-dependent semaphorin3A signaling.
Deo RC, Schmidt EF, Elhabazi A, Togashi H, Burley SK, Strittmatter SM
EMBO Journal (2004) , 23(1), 9-22
(Details) (Pub Med ID: 14685275)
PDB ID(s): 1KCXTimes cited: 62 - Crystal structure of YdcE protein from Bacillus subtilis.
Gogos A, Mu H, Bahna F, Gomez CA, Shapiro L
Proteins (2003) , 53(2), 320-2
(Details) (Pub Med ID: 14517982)
PDB ID(s): 1NE8Times cited: 10 - Crystal structure of shikimate 5-dehydrogenase (SDH) bound to NADP: insights into function and evolution.
Padyana AK, Burley SK
Structure (2003) , 11(8), 1005-13
(Details) (Pub Med ID: 12906831)
PDB ID(s): 1NVTTimes cited: 21 - Crystal structure of a putative CN hydrolase from yeast.
Kumaran D, Eswaramoorthy S, Gerchman SE, Kycia H, Studier FW, Swaminathan S
Proteins (2003) , 52(2), 283-91
(Details) (Pub Med ID: 12833551)
PDB ID(s): 1F89Times cited: 32 - Crystal structure of the MazE/MazF complex: molecular bases of antidote-toxin recognition.
Kamada K, Hanaoka F, Burley SK
Molecular Cell (2003) , 11(4), 875-84
(Details) (Pub Med ID: 12718874)
PDB ID(s): 1UB4Times cited: 114 - Structure of a yeast hypothetical protein selected by a structural genomics approach.
Eswaramoorthy S, Gerchman S, Graziano V, Kycia H, Studier FW, Swaminathan S
Acta Crystallographica Section D: Biological Crystallography (2003) , 59(Pt 1), 127-35
(Details) (Pub Med ID: 12499548)
PDB ID(s): 1B54Times cited: 13 - Structure of Escherichia coli uridine phosphorylase at 2.0 A.
Burling FT, Kniewel R, Buglino JA, Chadha T, Beckwith A, Lima CD
Acta Crystallographica Section D: Biological Crystallography (2003) , 59(Pt 1), 73-6
(Details) (Pub Med ID: 12499542)
PDB ID(s): 1LX7Times cited: 20 - X-ray structure of an M. jannaschii DNA-binding protein: implications for antibiotic resistance in S. aureus.
Ray SS, Bonanno JB, Chen H, de Lencastre H, Wu S, Tomasz A, Burley SK
Proteins (2003) , 50(1), 170-3
(Details) (Pub Med ID: 12471609)
PDB ID(s): 1KU9Times cited: 9 - High-Throughput Structural Biology and Proteomics
Shi W, Ostrov D, Gerchman S, Kycia H, Studier FW, Edstrom W, Bresnick A, Ehrlich J, Blanchard J, Almo S, Chance MR
Protein Arrays, Biochips and Proteomics: The Next Phase of Genomics Discovery, Marcel Dekker, Inc., New York, Chapter 12. (2003) Protein Arrays, Biochips and Proteomics: The Next Phase of Genomics Discovery, Marcel Dekker, Inc., New York, Chapter 12.
(Details)
Times cited: no data - Structural analysis of Saccharomyces cerevisiae myo-inositol phosphate synthase.
Kniewel R, Buglino JA, Shen V, Chadha T, Beckwith A, Lima CD
Journal of Structural and Functional Genomics (2002) , 2(3), 129-34
(Details) (Pub Med ID: 12836703)
PDB ID(s): 1LA2Times cited: 7 - Large conformational changes in the catalytic cycle of glutathione synthase.
Gogos A, Shapiro L
Structure (2002) , 10(12), 1669-76
(Details) (Pub Med ID: 12467574)
PDB ID(s): 1M0TTimes cited: 17 - Structural and biochemical analysis of the Obg GTP binding protein.
Buglino J, Shen V, Hakimian P, Lima CD
Structure (2002) , 10(11), 1581-92
(Details) (Pub Med ID: 12429099)Times cited: 62 - Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor.
Ray SS, Bonanno JB, Rajashankar KR, Pinho MG, He G, De Lencastre H, Tomasz A, Burley SK
Structure (2002) , 10(11), 1499-508
(Details) (Pub Med ID: 12429091)
PDB ID(s): 1TUFTimes cited: 23 - X-ray structures of threonine aldolase complexes: structural basis of substrate recognition.
Kielkopf CL, Burley SK
Biochemistry (2002) , 41(39), 11711-20
(Details) (Pub Med ID: 12269813)
PDB ID(s): 1LW4Times cited: 15 - X-ray structure of Saccharomyces cerevisiae homologous mitochondrial matrix factor 1 (Hmf1).
Deaconescu AM, Roll-Mecak A, Bonanno JB, Gerchman SE, Kycia H, Studier FW, Burley SK
Proteins (2002) , 48(2), 431-6
(Details) (Pub Med ID: 12112709)
PDB ID(s): 1JD1Times cited: 11 - Crystal structure of the Mus musculus cholesterol-regulated START protein 4 (StarD4) containing a StAR-related lipid transfer domain.
Romanowski MJ, Soccio RE, Breslow JL, Burley SK
Proceedings of the National Academy of Sciences of the United States of America (2002) , 99(10), 6949-54
(Details) (Pub Med ID: 12011453)
PDB ID(s): 1JSSTimes cited: 77 - Crystal structure of the Streptococcus pneumoniae phosphomevalonate kinase, a member of the GHMP kinase superfamily.
Romanowski MJ, Bonanno JB, Burley SK
Proteins (2002) , 47(4), 568-71
(Details) (Pub Med ID: 12001237)
PDB ID(s): 1K47Times cited: 37 - Crystal structure of the Escherichia coli glucose-inhibited division protein B (GidB) reveals a methyltransferase fold.
Romanowski MJ, Bonanno JB, Burley SK
Proteins (2002) , 47(4), 563-7
(Details) (Pub Med ID: 12001236)
PDB ID(s): 1JSXTimes cited: 13 - Crystal structure of the Escherichia coli shikimate kinase I (AroK) that confers sensitivity to mecillinam.
Romanowski MJ, Burley SK
Proteins (2002) , 47(4), 558-62
(Details) (Pub Med ID: 12001235)
PDB ID(s): 1KAGTimes cited: 21 - Crystal structure of the Escherichia coli SbmC protein that protects cells from the DNA replication inhibitor microcin B17.
Romanowski MJ, Gibney SA, Burley SK
Proteins (2002) , 47(3), 403-7
(Details) (Pub Med ID: 11948793)
PDB ID(s): 1JYHTimes cited: 11 - Structural genomics: a pipeline for providing structures for the biologist.
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
Protein Science (2002) , 11(4), 723-38
(Details) (Pub Med ID: 11910018)
PDB ID(s): 1JR7Times cited: 111 - Analysis of the E. coli NifS CsdB protein at 2.0 A reveals the structural basis for perselenide and persulfide intermediate formation.
Lima CD
Journal of Molecular Biology (2002) , 315(5), 1199-208
(Details) (Pub Med ID: 11827487)
PDB ID(s): 1KMJTimes cited: 47 - Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis.
Bonanno JB, Edo C, Eswar N, Pieper U, Romanowski MJ, Ilyin V, Gerchman SE, Kycia H, Studier FW, Sali A, Burley SK
Proceedings of the National Academy of Sciences of the United States of America (2001) , 98(23), 12896-901
(Details) (Pub Med ID: 11698677)
PDB ID(s): 1I9ATimes cited: 71 - Crystal structure of negative cofactor 2 recognizing the TBP-DNA transcription complex.
Kamada K, Shu F, Chen H, Malik S, Stelzer G, Roeder RG, Meisterernst M, Burley SK
Cell (2001) , 106(1), 71-81
(Details) (Pub Med ID: 11461703)
PDB ID(s): 1JFITimes cited: 76 - Crystal structures of ribosome anti-association factor IF6.
Groft CM, Beckmann R, Sali A, Burley SK
Nature Structural & Molecular Biology (2000) , 7(12), 1156-64
(Details) (Pub Med ID: 11101899)
PDB ID(s): 1G62Times cited: 30
2011 (click to unfold)
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Average number of citations per publication (structural): 22.1
Methodological and Other Publications
- Metalloproteomics: forward and reverse approaches in metalloprotein structural and functional characterization.
Shi W, Chance MR
Current Opinion in Chemical Biology (2011) , 15, 144-8
(Details) (Pub Med ID: 21130021)Times cited: 3 - ModBase, a database of annotated comparative protein structure models, and associated resources.
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
Nucleic Acids Research (2010) , 39, D465-74
(Details) (Pub Med ID: 21097780)
Times cited: no data - Mass spectrometry guided in situ proteolysis to obtain crystals for X-ray structure determination.
Gheyi T, Rodgers L, Romero R, Sauder JM, Burley SK
Journal of the American Society for Mass Spectrometry (2010) , 21, 1795-801
(Details) (Pub Med ID: 20685133)Times cited: 1 - Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies.
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
Journal of Structural and Functional Genomics (2009) , 10, 107-25
(Details) (Pub Med ID: 19219566)Times cited: 9 - Outcome of a workshop on applications of protein models in biomedical research.
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
Structure (2009) , 17, 151-9
(Details) (Pub Med ID: 19217386)Times cited: 27 - Structural genomics is the largest contributor of novel structural leverage.
Nair R, Liu J, Soong TT, Acton TB, Everett JK, Kouranov A, Fiser A, Godzik A, Jaroszewski L, Orengo C, Montelione GT, Rost B
Journal of Structural and Functional Genomics (2009) , 10, 181-91
(Details) (Pub Med ID: 19194785)Times cited: 28 - Improved scoring function for comparative modeling using the M4T method.
Rykunov D, Steinberger E, Madrid-Aliste CJ, Fiser A
Journal of Structural and Functional Genomics (2008) , 10, 95-9
(Details) (Pub Med ID: 18985440)
Times cited: no data - MODBASE, a database of annotated comparative protein structure models and associated resources.
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
Nucleic Acids Research (2008) , 37, D347-54
(Details) (Pub Med ID: 18948282)
Times cited: no data - Genomic-scale prioritization of drug targets: the TDR Targets database.
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
Nature reviews. Drug discovery (2008) , 7, 900-7
(Details) (Pub Med ID: 18927591)Times cited: 77 - How well can the accuracy of comparative protein structure models be predicted?
Eramian D, Eswar N, Shen MY, Sali A
Protein Science (2008) , 17, 1881-93
(Details) (Pub Med ID: 18832340)Times cited: 26 - Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies.
Chiang RA, Sali A, Babbitt PC
PLoS Computational Biology (2008) , 4, e1000142
(Details) (Pub Med ID: 18670595)Times cited: 14 - Metallomics and metalloproteomics.
Shi W, Chance MR
Cellular and Molecular Life Science (2008) , 65, 3040-8
(Details) (Pub Med ID: 18560755)Times cited: 54 - High throughput protein production and crystallization at NYSGXRC.
Sauder MJ, Rutter ME, Bain K, Rooney I, Gheyi T, Atwell S, Thompson DA, Emtage S, Burley SK
Methods in Molecular Biology (2008) , 426, 561-75
(Details) (Pub Med ID: 18542890)Times cited: 7 - Protein structure modeling with MODELLER.
Eswar N, Eramian D, Webb B, Shen MY, Sali A
Methods in Molecular Biology (2008) , 426, 145-59
(Details) (Pub Med ID: 18542861)Times cited: 159 - Prediction of enzyme function by combining sequence similarity and protein interactions.
Espadaler J, Eswar N, Querol E, Avilés FX, Sali A, Marti-Renom MA, Oliva B
BMC Bioinformatics (2008) , 9, 249
(Details) (Pub Med ID: 18505562)Times cited: 8 - Protein structure fitting and refinement guided by cryo-EM density.
Topf M, Lasker K, Webb B, Wolfson H, Chiu W, Sali A
Structure (2008) , 16(2), 295-307
(Details) (Pub Med ID: 18275820)Times cited: 66 - Protein production and purification.
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
Nature Methods (2008) , 5, 135-46
(Details) (Pub Med ID: 18235434)Times cited: 75 - Automated technologies and novel techniques to accelerate protein crystallography for structural genomics.
Manjasetty BA, Turnbull AP, Panjikar S, Büssow K, Chance MR
Proteomics (2008) , 8(4), 612-25
(Details) (Pub Med ID: 18210369)Times cited: 23 - Contributions to the NIH-NIGMS Protein Structure Initiative from the PSI Production Centers
Burley SK, Joachimiak A, Montelione GT, Wilson IA
Structure (2008) , 16(1), 5-11
(Details) (Pub Med ID: 18184575)Times cited: 28 - Comparative protein structure modeling using MODELLER.
Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A
Current Protocols in Protein Science (2007) , Chapter 2(11), Unit 2
(Details) (Pub Med ID: 18429317)
Times cited: 0 - Structural genomics.
Sali A, Lima CD, Kostic M
Structure (2007) , 15(11), 1341
(Details) (Pub Med ID: 17997955)Times cited: 2 - Host pathogen protein interactions predicted by comparative modeling.
Davis FP, Barkan DT, Eswar N, McKerrow JH, Sali A
Protein Science (2007) , 16(12), 2585-96
(Details) (Pub Med ID: 17965183)Times cited: 29 - Fold assessment for comparative protein structure modeling.
Melo F, Sali A
Protein Science (2007) , 16(11), 2412-26
(Details) (Pub Med ID: 17905832)Times cited: 20 - Modeling mutations in protein structures.
Feyfant E, Sali A, Fiser A
Protein Science (2007) , 16(9), 2030-41
(Details) (Pub Med ID: 17766392)Times cited: 17 - The AnnoLite and AnnoLyze programs for comparative annotation of protein structures.
Marti-Renom MA, Rossi A, Al-Shahrour F, Davis FP, Pieper U, Dopazo J, Sali A
BMC Bioinformatics (2007) , 8 Suppl 4(2), S4
(Details) (Pub Med ID: 17570147)Times cited: 15 - DBAli tools: mining the protein structure space.
Marti-Renom MA, Pieper U, Madhusudhan MS, Rossi A, Eswar N, Davis FP, Al-Shahrour F, Dopazo J, Sali A
Nucleic Acids Research (2007) , 35(Web Server issue), W393-7
(Details) (Pub Med ID: 17478513)Times cited: 15 - A high-throughput approach to protein structure analysis.
Manjasetty BA, Shi W, Zhan C, Fiser A, Chance MR
Genetic Engineering (2007) , 28, 105-28
(Details) (Pub Med ID: 17153936)Times cited: 7 - Structural Genomics at the National Synchrotron Light Source
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
2001 National Synchrotron Light Source Activity Report, 2-28 to 2-32. (2007) , 28, 105-28
(Details) (Pub Med ID: 17153936)
Times cited: no data - Structural modeling of protein interactions by analogy: application to PSD-95.
Korkin D, Davis FP, Alber F, Luong T, Shen MY, Lucic V, Kennedy MB, Sali A
PLoS Computational Biology (2006) , 2(11), e153
(Details) (Pub Med ID: 17096593)Times cited: 21 - Statistical potential for assessment and prediction of protein structures.
Shen MY, Sali A
Protein Science (2006) , 15(11), 2507-24
(Details) (Pub Med ID: 17075131)Times cited: 277 - Minimalist representations and the importance of nearest neighbor effects in protein folding simulations.
Colubri A, Jha AK, Shen MY, Sali A, Berry RS, Sosnick TR, Freed KF
Journal of Molecular Biology (2006) , 363(4), 835-57
(Details) (Pub Med ID: 16982067)Times cited: 16 - Localization of binding sites in protein structures by optimization of a composite scoring function.
Rossi A, Marti-Renom MA, Sali A
Protein Science (2006) , 15(10), 2366-80
(Details) (Pub Med ID: 16963645)Times cited: 10 - Outcome of a workshop on archiving structural models of biological macromolecules.
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
Structure (2006) , 14, 1211-7
(Details) (Pub Med ID: 16955948)
PDB ID(s): Times cited: 15 - MMM: a sequence-to-structure alignment protocol.
Rai BK, Madrid-Aliste CJ, Fajardo JE, Fiser A
Bioinformatics (2006) , 22(21), 2691-2
(Details) (Pub Med ID: 16928737)Times cited: 12 - ArchPRED: a template based loop structure prediction server.
Fernandez-Fuentes N, Zhai J, Fiser A
Nucleic Acids Research (2006) , 34(Web Server issue), W173-6
(Details) (Pub Med ID: 16844985)Times cited: 19 - Saturating representation of loop conformational fragments in structure databanks.
Fernandez-Fuentes N, Fiser A
BMC Structural Biology (2006) , 6(7), 15
(Details) (Pub Med ID: 16820050)Times cited: 10 - A composite score for predicting errors in protein structure models.
Eramian D, Shen MY, Devos D, Melo F, Sali A, Marti-Renom MA
Protein Science (2006) , 15(7), 1653-66
(Details) (Pub Med ID: 16751606)Times cited: 70 - Protein complex compositions predicted by structural similarity.
Davis FP, Braberg H, Shen MY, Pieper U, Sali A, Madhusudhan MS
Nucleic Acids Research (2006) , 34(10), 2943-52
(Details) (Pub Med ID: 16738133)Times cited: 23 - A supersecondary structure library and search algorithm for modeling loops in protein structures.
Fernandez-Fuentes N, Oliva B, Fiser A
Nucleic Acids Research (2006) , 34(7), 2085-97
(Details) (Pub Med ID: 16617149)Times cited: 23 - Structural biology of cellular machines.
Chiu W, Baker ML, Almo SC
Trends in Cell Biology (2006) , 16(3), 144-50
(Details) (Pub Med ID: 16459078)Times cited: 28 - Multiple mapping method: a novel approach to the sequence-to-structure alignment problem in comparative protein structure modeling.
Rai BK, Fiser A
Proteins (2006) , 63(3), 644-61
(Details) (Pub Med ID: 16437570)Times cited: 30 - Variable gap penalty for protein sequence-structure alignment.
Madhusudhan MS, Marti-Renom MA, Sanchez R, Sali A
Protein Engineering, Design and Selection (2006) , 19(3), 129-33
(Details) (Pub Med ID: 16423846)Times cited: 22 - MODBASE: a database of annotated comparative protein structure models and associated resources.
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
Nucleic Acids Research (2006) , 34(Database issue), D291-5
(Details) (Pub Med ID: 16381869)Times cited: 137 - Comparative Modeling of Drug Target Proteins
Eswar N, Sali A
Comprehensive Medicinal Chemistry, J. Taylor, and D. Triggle, eds. (Elsevier). (2006) Comprehensive Medicinal Chemistry, J. Taylor, and D. Triggle, eds. (Elsevier).
(Details)
Times cited: no data - Comparative Protein Structure Modeling with MODELLER
Eswar N, Marti-Renom MA
Current Protocols in Bioinformatics, I. John Wiley & Sons, ed. (2006) Current Protocols in Bioinformatics, I. John Wiley & Sons, ed.
(Details)
Times cited: 0 - Structural Genomics: high-throughput methods in structure determination of protein domains
Shi W, Chance MR
Comprehensive Medicinal Chemistry II, Volume 3: Drug Discovery Technologies, C. Hansch, Ed., Elsevier (2006) Comprehensive Medicinal Chemistry II, Volume 3: Drug Discovery Technologies, C. Hansch, Ed., Elsevier
(Details)
Times cited: no data - Metalloproteomics: high-throughput structural and functional annotation of proteins in structural genomics.
Shi W, Zhan C, Ignatov A, Manjasetty BA, Marinkovic N, Sullivan M, Huang R, Chance MR
Structure (2005) , 13(10), 1473-86
(Details) (Pub Med ID: 16216579)Times cited: 47 - New York-Structural GenomiX Research Consortium (NYSGXRC): a large scale center for the protein structure initiative.
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
Journal of Structural and Functional Genomics (2005) , 6(2-3), 225-32
(Details) (Pub Med ID: 16211523)Times cited: 20 - High-throughput limited proteolysis/mass spectrometry for protein domain elucidation.
Gao X, Bain K, Bonanno JB, Buchanan M, Henderson D, Lorimer D, Marsh C, Reynes JA, Sauder JM, Schwinn K, Thai C, Burley SK
Journal of Structural and Functional Genomics (2005) , 6(2-3), 129-34
(Details) (Pub Med ID: 16211509)Times cited: 31 - Radiation-induced site-specific damage of mercury derivatives: phasing and implications.
Ramagopal UA, Dauter Z, Thirumuruhan R, Fedorov E, Almo SC
Acta Crystallographica Section D: Biological Crystallography (2005) , 61(Pt 9), 1289-98
(Details) (Pub Med ID: 16131763)Times cited: 25 - Protein production by auto-induction in high density shaking cultures.
Studier FW
Protein Expression and Purification (2005) , 41(1), 207-34
(Details) (Pub Med ID: 15915565)Times cited: 951 - The Bacillus subtilis ydcDE operon encodes an endoribonuclease of the MazF/PemK family and its inhibitor.
Pellegrini O, Mathy N, Gogos A, Shapiro L, Condon C
Molecular Microbiology (2005) , 56(5), 1139-48
(Details) (Pub Med ID: 15882409)Times cited: 27 - LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources.
Karchin R, Diekhans M, Kelly L, Thomas DJ, Pieper U, Eswar N, Haussler D, Sali A
Bioinformatics (2005) , 21(12), 2814-20
(Details) (Pub Med ID: 15827081)Times cited: 98 - Finding a cold needle in a warm haystack: infrared imaging applied to locating crycocooled crystals in loops
Snell EH, van der Woerd MJ, Miller MD, Deacon AM
Journal of Applied Crystallography (2005) , 38, 69-77
(Details)Times cited: 7 - Comparative Protein Structure Modeling
Sauder JM, Rutter ME, Bain K, Rooney I, Gheyi T, Atwell S, Thompson DA, Emtage S, Burley SK
The Proteomics Protocols Handbook. Ed: J.M. Walker. Humana Press Inc., Totowa, NJ. (2005) The Proteomics Protocols Handbook. Ed: J.M. Walker. Humana Press Inc., Totowa, NJ.
(Details)
Times cited: no data - High-throughput computational and experimental techniques in structural genomics.
Chance MR, Fiser A, Sali A, Pieper U, Eswar N, Xu G, Fajardo JE, Radhakannan T, Marinkovic N
Genome Research (2004) , 14(10B), 2145-54
(Details) (Pub Med ID: 15489337)Times cited: 46 - Optimization of protein production in mammalian cells with a coexpressed fluorescent marker.
Mancia F, Patel SD, Rajala MW, Scherer PE, Nemes A, Schieren I, Hendrickson WA, Shapiro L
Structure (2004) , 12(8), 1355-60
(Details) (Pub Med ID: 15296729)Times cited: 30 - Protein Data Bank depositions from synchrotron sources.
Jiang J, Sweet RM
Journal of Synchrotron Radiation (2004) , 11(Pt 4), 319-27
(Details) (Pub Med ID: 15211038)Times cited: 19 - Comprehensive search for cysteine cathepsins in the human genome.
Rossi A, Deveraux Q, Turk B, Sali A
Biological Chemistry (2004) , 385(5), 363-72
(Details) (Pub Med ID: 15195995)Times cited: 23 - Structure-based assessment of missense mutations in human BRCA1: implications for breast and ovarian cancer predisposition.
Mirkovic N, Marti-Renom MA, Weber BL, Sali A, Monteiro AN
Cancer Research (2004) , 64(11), 3790-7
(Details) (Pub Med ID: 15172985)Times cited: 55 - MODBASE, a database of annotated comparative protein structure models, and associated resources.
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
Nucleic Acids Research (2004) , 32(Database issue), D217-22
(Details) (Pub Med ID: 14681398)Times cited: 118 - Modeller: generation and refinement of homology-based protein structure models.
Fiser A, Sali A
Methods in Enzymology (2003) , 374(Pt 7), 461-91
(Details) (Pub Med ID: 14696385)Times cited: 322 - High-throughput expression, purification, and characterization of recombinant Caenorhabditis elegans proteins.
Huang RY, Boulton SJ, Vidal M, Almo SC, Bresnick AR, Chance MR
Biochemical and Biophysical Research Communications (2003) , 307(4), 928-34
(Details) (Pub Med ID: 12878200)Times cited: 15 - Comparative protein structure modeling by iterative alignment, model building and model assessment.
John B, Sali A
Nucleic Acids Research (2003) , 31(14), 3982-92
(Details) (Pub Med ID: 12853614)Times cited: 111 - Tools for comparative protein structure modeling and analysis.
Eswar N, John B, Mirkovic N, Fiser A, Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, Madhusudhan MS, Yerkovich B, Sali A
Nucleic Acids Research (2003) , 31(13), 3375-80
(Details) (Pub Med ID: 12824331)Times cited: 147 - EVA: Evaluation of protein structure prediction servers.
Koh IY, Eyrich VA, Marti-Renom MA, Przybylski D, Madhusudhan MS, Eswar N, Graña O, Pazos F, Valencia A, Sali A, Rost B
Nucleic Acids Research (2003) , 31(13), 3311-5
(Details) (Pub Med ID: 12824315)Times cited: 102 - Study of the structural dynamics of the E coli 70S ribosome using real-space refinement.
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
Cell (2003) , 113(6), 789-801
(Details) (Pub Med ID: 12809609)Times cited: 190 - C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression.
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
Nature Genetics (2003) , 34(1), 35-41
(Details) (Pub Med ID: 12679813)Times cited: 217 - Structural genomics.
Burley SK, Bonanno JB
Methods of Biochemical Analysis (2003) , 44(2-3), 591-612
(Details) (Pub Med ID: 12647406)Times cited: 22 - From words to literature in structural proteomics.
Sali A, Glaeser R, Earnest T, Baumeister W
Nature (2003) , 422(6928), 216-25
(Details) (Pub Med ID: 12634795)Times cited: 260 - ModView, visualization of multiple protein sequences and structures.
Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, McMahan L, Sali A
Bioinformatics (2003) , 19(1), 165-6
(Details) (Pub Med ID: 12499313)Times cited: 7 - The kinetic mechanism of phosphomevalonate kinase.
Pilloff D, Dabovic K, Romanowski MJ, Bonanno JB, Doherty M, Burley SK, Leyh TS
Journal of Biological Chemistry (2003) , 278(7), 4510-5
(Details) (Pub Med ID: 12424232)Times cited: 26 - Modeling protein structure from its sequence
Marti-Renom MA, Fiser A, Madhusudhan MS, John B, Stuart A, Eswar N, Pieper P, Shen MY, Sali A
Current Protocols in Bioinformatics John Wiley & Sons, Inc., V. 5 November Issue. (2003) Current Protocols in Bioinformatics John Wiley & Sons, Inc., V. 5 November Issue.
(Details)
Times cited: no data - Structuring the universe of proteins.
Burley SK, Bonanno JB
Annual Review of Genomics and Human Genetics (2002) , 3(12), 243-62
(Details) (Pub Med ID: 12194989)Times cited: 42 - Structural genomics of proteins from conserved biochemical pathways and processes.
Burley SK, Bonanno JB
Current Opinion in Structural Biology (2002) , 12(3), 383-91
(Details) (Pub Med ID: 12127459)Times cited: 25 - Evolution and physics in comparative protein structure modeling.
Fiser A, Feig M, Brooks CL, Sali A
Accounts of Chemical Research (2002) , 35(6), 413-21
(Details) (Pub Med ID: 12069626)Times cited: 57 - The cholesterol-regulated StarD4 gene encodes a StAR-related lipid transfer protein with two closely related homologues, StarD5 and StarD6.
Soccio RE, Adams RM, Romanowski MJ, Sehayek E, Burley SK, Breslow JL
Proceedings of the National Academy of Sciences of the United States of America (2002) , 99(10), 6943-8
(Details) (Pub Med ID: 12011452)Times cited: 76 - Reliability of assessment of protein structure prediction methods.
Marti-Renom MA, Madhusudhan MS, Fiser A, Rost B, Sali A
Structure (2002) , 10(3), 435-40
(Details) (Pub Med ID: 12005441)Times cited: 53 - 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.
Yang Y, Li L, Wong GW, Krilis SA, Madhusudhan MS, Sali A, Stevens RL
Journal of Biological Chemistry (2002) , 277(28), 25756-74
(Details) (Pub Med ID: 11956218)Times cited: 61 - LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures.
Stuart AC, Ilyin VA, Sali A
Bioinformatics (2002) , 18(1), 200-1
(Details) (Pub Med ID: 11836232)Times cited: 48 - Statistical potentials for fold assessment.
Melo F, Sánchez R, Sali A
Protein Science (2002) , 11(2), 430-48
(Details) (Pub Med ID: 11790853)Times cited: 121 - MODBASE, a database of annotated comparative protein structure models.
Pieper U, Eswar N, Stuart AC, Ilyin VA, Sali A
Nucleic Acids Research (2002) , 30(1), 255-9
(Details) (Pub Med ID: 11752309)Times cited: 65 - Reply to Moult et al
Sali A, Marti-Renom MA, Madhusudhan MS, Fiser A, Rost B
Structure (2002) , 10, 292-293
(Details)
Times cited: no data - Comparative protein structure prediction
Sauder JM, Rutter ME, Bain K, Rooney I, Gheyi T, Atwell S, Thompson DA, Emtage S and Burley SK
Ed: John Wiley & Sons, Inc. Curr. Protocol. Prot. Sci. 1, 2.9.1-2.9.22. (2002) Ed: John Wiley & Sons, Inc. Curr. Protocol. Prot. Sci. 1, 2.9.1-2.9.22.
(Details)
Times cited: no data - Characterizing the relationship between protein-fusion and gene co-expression.
Gunther CS, Gaasterland T
Genome Informatics. International Conference on Genome Informatics (2001) , 12(Pt 2), 34-43
(Details) (Pub Med ID: 11791222)
Times cited: 0 - Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions.
Spahn CM, Beckmann R, Eswar N, Penczek PA, Sali A, Blobel G, Frank J
Cell (2001) , 107(3), 373-86
(Details) (Pub Med ID: 11701127)Times cited: 319 - Architecture of the protein-conducting channel associated with the translating 80S ribosome.
Beckmann R, Spahn CM, Eswar N, Helmers J, Penczek PA, Sali A, Frank J, Blobel G
Cell (2001) , 107(3), 361-72
(Details) (Pub Med ID: 11701126)Times cited: 243 - A functional update of the Escherichia coli K-12 genome.
Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M
Genome Biology (2001) , 2(9), RESEARCH0035
(Details) (Pub Med ID: 11574054)Times cited: 4 - DBAli: a database of protein structure alignments.
Marti-Renom MA, Ilyin VA, Sali A
Bioinformatics (2001) , 17(8), 746-7
(Details) (Pub Med ID: 11524379)Times cited: 31 - Whole-genome analysis: annotations and updates.
Gaasterland T, Oprea M
Current Opinion in Structural Biology (2001) , 11(3), 377-81
(Details) (Pub Med ID: 11406390)Times cited: 24 - Target practice.
Sali A
Nature Structural & Molecular Biology (2001) , 8(6), 482-4
(Details) (Pub Med ID: 11373610)Times cited: 20 - Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome.
Gopal S, Schroeder M, Pieper U, Sczyrba A, Aytekin-Kurban G, Bekiranov S, Fajardo JE, Eswar N, Sanchez R, Sali A, Gaasterland T
Nature Genetics (2001) , 27(3), 337-40
(Details) (Pub Med ID: 11242120)Times cited: 45 - Protein structure modeling for structural genomics.
Sánchez R, Pieper U, Melo F, Eswar N, Martí-Renom MA, Madhusudhan MS, Mirković N, Sali A
Nature Structural & Molecular Biology (2000) , 7 Suppl(41), 986-90
(Details) (Pub Med ID: 11104007)Times cited: 132 - An overview of structural genomics.
Burley SK
Nature Structural & Molecular Biology (2000) , 7 Suppl(5), 932-4
(Details) (Pub Med ID: 11103991)Times cited: 158 - Identification and characterization of a p53 homologue in Drosophila melanogaster.
Jin S, Martinek S, Joo WS, Wortman JR, Mirkovic N, Sali A, Yandell MD, Pavletich NP, Young MW, Levine AJ
Proceedings of the National Academy of Sciences of the United States of America (2000) , 97(13), 7301-6
(Details) (Pub Med ID: 10860994)Times cited: 123
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Average number of citations per publication (methodological): 63.0