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For: Laskowski RA, Watson JD, Thornton JM. From protein structure to biochemical function? ACTA ACUST UNITED AC 2004;4:167-77. [PMID: 14649301 DOI: 10.1023/a:1026127927612] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Number Cited by Other Article(s)
1
Abdollahi S, Raoufi Z. A novel vaccine candidate against A. baumannii based on a new OmpW family protein (OmpW2); structural characterization, antigenicity and epitope investigation, and in-vivo analysis. Microb Pathog 2023;183:106317. [PMID: 37611777 DOI: 10.1016/j.micpath.2023.106317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/06/2023] [Accepted: 08/20/2023] [Indexed: 08/25/2023]
2
Abdollahi S, Raoufi Z, Fakoor MH. Physicochemical and structural characterization, epitope mapping and vaccine potential investigation of a new protein containing Tetratrico Peptide Repeats of Acinetobacter baumannii: An in-silico and in-vivo approach. Mol Immunol 2021;140:22-34. [PMID: 34649027 DOI: 10.1016/j.molimm.2021.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 09/13/2021] [Accepted: 10/04/2021] [Indexed: 11/24/2022]
3
Selim KA, Tremiño L, Marco-Marín C, Alva V, Espinosa J, Contreras A, Hartmann MD, Forchhammer K, Rubio V. Functional and structural characterization of PII-like protein CutA does not support involvement in heavy metal tolerance and hints at a small-molecule carrying/signaling role. FEBS J 2020;288:1142-1162. [PMID: 32599651 DOI: 10.1111/febs.15464] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 04/26/2020] [Accepted: 06/01/2020] [Indexed: 12/23/2022]
4
An in silico structural and physicochemical characterization of TonB-dependent copper receptor in A. baumannii. Microb Pathog 2018. [DOI: 10.1016/j.micpath.2018.03.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
5
Ingale AG. Prediction of Structural and Functional Aspects of Protein. PHARMACEUTICAL SCIENCES 2017. [DOI: 10.4018/978-1-5225-1762-7.ch021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]  Open
6
In silico determination and validation of baumannii acinetobactin utilization a structure and ligand binding site. BIOMED RESEARCH INTERNATIONAL 2013;2013:172784. [PMID: 24106696 PMCID: PMC3780550 DOI: 10.1155/2013/172784] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Revised: 07/21/2013] [Accepted: 07/31/2013] [Indexed: 01/21/2023]
7
Wang Z, Yin P, Lee JS, Parasuram R, Somarowthu S, Ondrechen MJ. Protein function annotation with Structurally Aligned Local Sites of Activity (SALSAs). BMC Bioinformatics 2013;14 Suppl 3:S13. [PMID: 23514271 PMCID: PMC3584854 DOI: 10.1186/1471-2105-14-s3-s13] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]  Open
8
Sureshan V, Deshpande CN, Boucher Y, Koenig JE, Stokes HW, Harrop SJ, Curmi PMG, Mabbutt BC. Integron gene cassettes: a repository of novel protein folds with distinct interaction sites. PLoS One 2013;8:e52934. [PMID: 23349695 PMCID: PMC3548836 DOI: 10.1371/journal.pone.0052934] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2012] [Accepted: 11/26/2012] [Indexed: 11/19/2022]  Open
9
Han L, Zhang YJ, Song J, Liu MS, Zhang Z. Identification of catalytic residues using a novel feature that integrates the microenvironment and geometrical location properties of residues. PLoS One 2012;7:e41370. [PMID: 22829945 PMCID: PMC3400608 DOI: 10.1371/journal.pone.0041370] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 06/20/2012] [Indexed: 11/18/2022]  Open
10
Sleator RD. Proteins: form and function. Bioeng Bugs 2012;3:80-5. [PMID: 22095055 DOI: 10.4161/bbug.18303] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]  Open
11
Buchko GW, Robinson H. Crystal structure of cce_0566 from Cyanothece 51142, a protein associated with nitrogen fixation in the DUF269 family. FEBS Lett 2012;586:350-5. [PMID: 22289180 PMCID: PMC3641832 DOI: 10.1016/j.febslet.2012.01.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 01/16/2012] [Accepted: 01/16/2012] [Indexed: 11/24/2022]
12
Sleator RD. Prediction of protein functions. Methods Mol Biol 2012;815:15-24. [PMID: 22130980 DOI: 10.1007/978-1-61779-424-7_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
13
Doppelt-Azeroual O, Delfaud F, Moriaud F, de Brevern AG. Fast and automated functional classification with MED-SuMo: an application on purine-binding proteins. Protein Sci 2010;19:847-67. [PMID: 20162627 DOI: 10.1002/pro.364] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
14
Vorobjev YN. Blind docking method combining search of low-resolution binding sites with ligand pose refinement by molecular dynamics-based global optimization. J Comput Chem 2010;31:1080-92. [PMID: 19821514 DOI: 10.1002/jcc.21394] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
15
Buchko GW, Robinson H, Abendroth J, Staker BL, Myler PJ. Structural characterization of Burkholderia pseudomallei adenylate kinase (Adk): profound asymmetry in the crystal structure of the 'open' state. Biochem Biophys Res Commun 2010;394:1012-7. [PMID: 20331978 DOI: 10.1016/j.bbrc.2010.03.112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Accepted: 03/17/2010] [Indexed: 02/02/2023]
16
An overview of in silico protein function prediction. Arch Microbiol 2010;192:151-5. [DOI: 10.1007/s00203-010-0549-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Revised: 01/08/2010] [Accepted: 01/10/2010] [Indexed: 12/12/2022]
17
Buchko GW, Robinson H, Addlagatta A. Structural characterization of the protein cce_0567 from Cyanothece 51142, a metalloprotein associated with nitrogen fixation in the DUF683 family. BIOCHIMICA ET BIOPHYSICA ACTA 2009;1794:627-33. [PMID: 19336042 PMCID: PMC3707797 DOI: 10.1016/j.bbapap.2009.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2008] [Revised: 01/06/2009] [Accepted: 01/07/2009] [Indexed: 11/26/2022]
18
Liu ZP, Wu LY, Wang Y, Zhang XS, Chen L. Bridging protein local structures and protein functions. Amino Acids 2008;35:627-50. [PMID: 18421562 PMCID: PMC7088341 DOI: 10.1007/s00726-008-0088-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2008] [Accepted: 03/10/2008] [Indexed: 12/11/2022]
19
Peisach E, Wang L, Burroughs AM, Aravind L, Dunaway-Mariano D, Allen KN. The X-ray crystallographic structure and activity analysis of a Pseudomonas-specific subfamily of the HAD enzyme superfamily evidences a novel biochemical function. Proteins 2008;70:197-207. [PMID: 17654544 DOI: 10.1002/prot.21583] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
20
Jianlin Cheng, Tegge A, Baldi P. Machine Learning Methods for Protein Structure Prediction. IEEE Rev Biomed Eng 2008;1:41-9. [DOI: 10.1109/rbme.2008.2008239] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
21
Harris R, Olson AJ, Goodsell DS. Automated prediction of ligand-binding sites in proteins. Proteins 2007;70:1506-17. [PMID: 17910060 DOI: 10.1002/prot.21645] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
22
Koclega KD, Chruszcz M, Zimmerman MD, Cymborowski M, Evdokimova E, Minor W. Crystal structure of a transcriptional regulator TM1030 from Thermotoga maritima solved by an unusual MAD experiment. J Struct Biol 2007;159:424-32. [PMID: 17588774 PMCID: PMC2093942 DOI: 10.1016/j.jsb.2007.04.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Revised: 04/20/2007] [Accepted: 04/30/2007] [Indexed: 01/07/2023]
23
Sangar V, Blankenberg DJ, Altman N, Lesk AM. Quantitative sequence-function relationships in proteins based on gene ontology. BMC Bioinformatics 2007;8:294. [PMID: 17686158 PMCID: PMC1976327 DOI: 10.1186/1471-2105-8-294] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2007] [Accepted: 08/08/2007] [Indexed: 11/10/2022]  Open
24
Bertini I, Rosato A. From Genes to Metalloproteins: A Bioinformatic Approach. Eur J Inorg Chem 2007. [DOI: 10.1002/ejic.200700186] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
25
Marti-Renom MA, Rossi A, Al-Shahrour F, Davis FP, Pieper U, Dopazo J, Sali A. The AnnoLite and AnnoLyze programs for comparative annotation of protein structures. BMC Bioinformatics 2007;8 Suppl 4:S4. [PMID: 17570147 PMCID: PMC1892083 DOI: 10.1186/1471-2105-8-s4-s4] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
26
Marti-Renom MA, Pieper U, Madhusudhan MS, Rossi A, Eswar N, Davis FP, Al-Shahrour F, Dopazo J, Sali A. DBAli tools: mining the protein structure space. Nucleic Acids Res 2007;35:W393-7. [PMID: 17478513 PMCID: PMC1933139 DOI: 10.1093/nar/gkm236] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
27
Kawabata T, Go N. Detection of pockets on protein surfaces using small and large probe spheres to find putative ligand binding sites. Proteins 2007;68:516-29. [PMID: 17444522 DOI: 10.1002/prot.21283] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
28
Marsden RL, Lewis TA, Orengo CA. Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint. BMC Bioinformatics 2007;8:86. [PMID: 17349043 PMCID: PMC1829165 DOI: 10.1186/1471-2105-8-86] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Accepted: 03/09/2007] [Indexed: 11/25/2022]  Open
29
Lesnyak DV, Osipiuk J, Skarina T, Sergiev PV, Bogdanov AA, Edwards A, Savchenko A, Joachimiak A, Dontsova OA. Methyltransferase that modifies guanine 966 of the 16 S rRNA: functional identification and tertiary structure. J Biol Chem 2007;282:5880-7. [PMID: 17189261 PMCID: PMC2885967 DOI: 10.1074/jbc.m608214200] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
30
Andreini C, Banci L, Bertini I, Rosato A. Zinc through the three domains of life. J Proteome Res 2007;5:3173-8. [PMID: 17081069 DOI: 10.1021/pr0603699] [Citation(s) in RCA: 443] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
31
Rossi A, Marti-Renom MA, Sali A. Localization of binding sites in protein structures by optimization of a composite scoring function. Protein Sci 2006;15:2366-80. [PMID: 16963645 PMCID: PMC2242385 DOI: 10.1110/ps.062247506] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
32
Osipiuk J, Maltseva N, Dementieva I, Clancy S, Collart F, Joachimiak A. Structure of YidB protein from Shigella flexneri shows a new fold with homeodomain motif. Proteins 2006;65:509-13. [PMID: 16927377 PMCID: PMC2885951 DOI: 10.1002/prot.21054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
33
Deng H, Chen G, Yang W, Yang JJ. Predicting calcium-binding sites in proteins - a graph theory and geometry approach. Proteins 2006;64:34-42. [PMID: 16617426 DOI: 10.1002/prot.20973] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
34
Kim Y, Maltseva N, Dementieva I, Collart F, Holzle D, Joachimiak A. Crystal structure of hypothetical protein YfiH from Shigella flexneri at 2 A resolution. Proteins 2006;63:1097-101. [PMID: 16498617 PMCID: PMC2792012 DOI: 10.1002/prot.20589] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
35
Nocek B, Cuff M, Evdokimova E, Edwards A, Joachimiak A, Savchenko A. 1.6 A crystal structure of a PA2721 protein from pseudomonas aeruginosa--a potential drug-resistance protein. Proteins 2006;63:1102-5. [PMID: 16493657 PMCID: PMC2792011 DOI: 10.1002/prot.20659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
36
Yura K, Yamaguchi A, Go M. Coverage of whole proteome by structural genomics observed through protein homology modeling database. JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS 2006;7:65-76. [PMID: 17146617 PMCID: PMC1769342 DOI: 10.1007/s10969-006-9010-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2006] [Accepted: 08/08/2006] [Indexed: 11/07/2022]
37
Zhang R, Minh T, Lezondra L, Korolev S, Moy S, Collart F, Joachimiak A. 1.6 A crystal structure of YteR protein from Bacillus subtilis, a predicted lyase. Proteins 2006;60:561-5. [PMID: 15906318 PMCID: PMC2792013 DOI: 10.1002/prot.20410] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
38
Fleming K, Kelley LA, Islam SA, MacCallum RM, Muller A, Pazos F, Sternberg MJ. The proteome: structure, function and evolution. Philos Trans R Soc Lond B Biol Sci 2006;361:441-51. [PMID: 16524832 PMCID: PMC1609342 DOI: 10.1098/rstb.2005.1802] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
39
Ferré S, King RD. Finding Motifs in Protein Secondary Structure for Use in Function Prediction. J Comput Biol 2006;13:719-31. [PMID: 16706721 DOI: 10.1089/cmb.2006.13.719] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
40
Ofran Y, Punta M, Schneider R, Rost B. Beyond annotation transfer by homology: novel protein-function prediction methods to assist drug discovery. Drug Discov Today 2006;10:1475-82. [PMID: 16243268 DOI: 10.1016/s1359-6446(05)03621-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
41
Castrignanò T, De Meo PD, Cozzetto D, Talamo IG, Tramontano A. The PMDB Protein Model Database. Nucleic Acids Res 2006;34:D306-9. [PMID: 16381873 PMCID: PMC1347467 DOI: 10.1093/nar/gkj105] [Citation(s) in RCA: 230] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]  Open
42
Marsden RL, Lee D, Maibaum M, Yeats C, Orengo CA. Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space. Nucleic Acids Res 2006;34:1066-80. [PMID: 16481312 PMCID: PMC1373602 DOI: 10.1093/nar/gkj494] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]  Open
43
Gold ND, Jackson RM. Fold Independent Structural Comparisons of Protein–Ligand Binding Sites for Exploring Functional Relationships. J Mol Biol 2006;355:1112-24. [PMID: 16359705 DOI: 10.1016/j.jmb.2005.11.044] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2005] [Revised: 11/11/2005] [Accepted: 11/15/2005] [Indexed: 11/23/2022]
44
Zhang Z, Grigorov MG. Similarity networks of protein binding sites. Proteins 2005;62:470-8. [PMID: 16299776 DOI: 10.1002/prot.20752] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
45
Najmanovich RJ, Torrance JW, Thornton JM. Prediction of protein function from structure: insights from methods for the detection of local structural similarities. Biotechniques 2005;38:847, 849, 851. [PMID: 16018542 DOI: 10.2144/05386te01] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]  Open
46
Takeuchi H, Rigden DJ, Ebrahimi B, Turner PC, Rees HH. Regulation of ecdysteroid signalling during Drosophila development: identification, characterization and modelling of ecdysone oxidase, an enzyme involved in control of ligand concentration. Biochem J 2005;389:637-45. [PMID: 15813704 PMCID: PMC1180713 DOI: 10.1042/bj20050498] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
47
Valencia A. Automatic annotation of protein function. Curr Opin Struct Biol 2005;15:267-74. [PMID: 15922590 DOI: 10.1016/j.sbi.2005.05.010] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2005] [Revised: 04/29/2005] [Accepted: 05/10/2005] [Indexed: 11/22/2022]
48
Laskowski RA, Watson JD, Thornton JM. ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res 2005;33:W89-93. [PMID: 15980588 PMCID: PMC1160175 DOI: 10.1093/nar/gki414] [Citation(s) in RCA: 471] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]  Open
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Watson JD, Laskowski RA, Thornton JM. Predicting protein function from sequence and structural data. Curr Opin Struct Biol 2005;15:275-84. [PMID: 15963890 DOI: 10.1016/j.sbi.2005.04.003] [Citation(s) in RCA: 203] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2005] [Revised: 02/04/2005] [Accepted: 04/18/2005] [Indexed: 10/25/2022]
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Crystal structure of the hypothetical protein TA1238 from Thermoplasma acidophilum: a new type of helical super-bundle. ACTA ACUST UNITED AC 2005. [DOI: 10.1007/s10969-004-3789-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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