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For: Wallace AC, Borkakoti N, Thornton JM. TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites. Protein Sci 1997;6:2308-23. [PMID: 9385633 PMCID: PMC2143595 DOI: 10.1002/pro.5560061104] [Citation(s) in RCA: 257] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Number Cited by Other Article(s)
1
Riziotis IG, Ribeiro AJM, Borkakoti N, Thornton JM. The 3D Modules of Enzyme Catalysis: Deconstructing Active Sites into Distinct Functional Entities. J Mol Biol 2023;435:168254. [PMID: 37652131 DOI: 10.1016/j.jmb.2023.168254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/20/2023] [Accepted: 08/22/2023] [Indexed: 09/02/2023]
2
Shen X, Zhang S, Long J, Chen C, Wang M, Cui Z, Chen B, Tan T. A Highly Sensitive Model Based on Graph Neural Networks for Enzyme Key Catalytic Residue Prediction. J Chem Inf Model 2023;63:4277-4290. [PMID: 37399293 DOI: 10.1021/acs.jcim.3c00273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
3
Eguida M, Rognan D. Estimating the Similarity between Protein Pockets. Int J Mol Sci 2022;23:12462. [PMID: 36293316 PMCID: PMC9604425 DOI: 10.3390/ijms232012462] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/15/2022] [Accepted: 10/16/2022] [Indexed: 10/28/2023]  Open
4
Riziotis IG, Thornton JM. Capturing the geometry, function, and evolution of enzymes with 3D templates. Protein Sci 2022;31:e4363. [PMID: 35762726 PMCID: PMC9207746 DOI: 10.1002/pro.4363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/06/2022] [Accepted: 05/14/2022] [Indexed: 11/05/2022]
5
Lu Q. Identifying molecular structural features by pattern recognition methods. RSC Adv 2022;12:17559-17569. [PMID: 35765452 PMCID: PMC9192268 DOI: 10.1039/d2ra00764a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 06/06/2022] [Indexed: 11/21/2022]  Open
6
Riziotis IG, Ribeiro AJ, Borkakoti N, Thornton JM. Conformational variation in enzyme catalysis: A structural study on catalytic residues. J Mol Biol 2022;434:167517. [PMID: 35240125 PMCID: PMC9005782 DOI: 10.1016/j.jmb.2022.167517] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/21/2022] [Accepted: 02/23/2022] [Indexed: 11/26/2022]
7
Lu Q. Molecular structure recognition by blob detection. RSC Adv 2021;11:35879-35886. [PMID: 35492772 PMCID: PMC9043223 DOI: 10.1039/d1ra05752a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/31/2021] [Indexed: 11/23/2022]  Open
8
Das S, Scholes HM, Sen N, Orengo C. CATH functional families predict functional sites in proteins. Bioinformatics 2021;37:1099-1106. [PMID: 33135053 PMCID: PMC8150129 DOI: 10.1093/bioinformatics/btaa937] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 09/30/2020] [Accepted: 10/27/2020] [Indexed: 01/12/2023]  Open
9
A mathematical representation of protein binding sites using structural dispersion of atoms from principal axes for classification of binding ligands. PLoS One 2021;16:e0244905. [PMID: 33831020 PMCID: PMC8031081 DOI: 10.1371/journal.pone.0244905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/09/2021] [Indexed: 11/23/2022]  Open
10
Ireland SM, Martin ACR. Zincbindpredict-Prediction of Zinc Binding Sites in Proteins. Molecules 2021;26:molecules26040966. [PMID: 33673040 PMCID: PMC7918553 DOI: 10.3390/molecules26040966] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/26/2021] [Accepted: 02/09/2021] [Indexed: 11/21/2022]  Open
11
Bittrich S, Burley SK, Rose AS. Real-time structural motif searching in proteins using an inverted index strategy. PLoS Comput Biol 2020;16:e1008502. [PMID: 33284792 PMCID: PMC7746303 DOI: 10.1371/journal.pcbi.1008502] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 12/17/2020] [Accepted: 11/09/2020] [Indexed: 12/30/2022]  Open
12
Torng W, Altman RB. High precision protein functional site detection using 3D convolutional neural networks. Bioinformatics 2020;35:1503-1512. [PMID: 31051039 PMCID: PMC6499237 DOI: 10.1093/bioinformatics/bty813] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 08/14/2018] [Accepted: 09/19/2018] [Indexed: 12/02/2022]  Open
13
Rey J, Rasolohery I, Tufféry P, Guyon F, Moroy G. PatchSearch: a web server for off-target protein identification. Nucleic Acids Res 2020;47:W365-W372. [PMID: 31131411 PMCID: PMC6602448 DOI: 10.1093/nar/gkz478] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/26/2019] [Accepted: 05/21/2019] [Indexed: 01/17/2023]  Open
14
Ribeiro AJM, Holliday GL, Furnham N, Tyzack JD, Ferris K, Thornton JM. Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites. Nucleic Acids Res 2019;46:D618-D623. [PMID: 29106569 PMCID: PMC5753290 DOI: 10.1093/nar/gkx1012] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 10/13/2017] [Indexed: 12/28/2022]  Open
15
Kaiser F, Labudde D. Unsupervised Discovery of Geometrically Common Structural Motifs and Long-Range Contacts in Protein 3D Structures. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019;16:671-680. [PMID: 29990265 DOI: 10.1109/tcbb.2017.2786250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
16
Jiang T, Renfrew PD, Drew K, Youngs N, Butterfoss GL, Bonneau R, Shasha DN. An adaptive geometric search algorithm for macromolecular scaffold selection. Protein Eng Des Sel 2018;31:345-354. [PMID: 30407584 PMCID: PMC6373690 DOI: 10.1093/protein/gzy028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 10/05/2018] [Indexed: 11/14/2022]  Open
17
Muthu Krishnan S. Using Chou's general PseAAC to analyze the evolutionary relationship of receptor associated proteins (RAP) with various folding patterns of protein domains. J Theor Biol 2018;445:62-74. [DOI: 10.1016/j.jtbi.2018.02.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/24/2018] [Accepted: 02/12/2018] [Indexed: 01/31/2023]
18
Anders G, Hassiepen U, Theisgen S, Heymann S, Muller L, Panigada T, Huster D, Samsonov SA. The Intrinsic Pepsin Resistance of Interleukin-8 Can Be Explained from a Combined Bioinformatical and Experimental Approach. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018;15:300-308. [PMID: 28113517 DOI: 10.1109/tcbb.2016.2614821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
19
Sánchez DA, Tonetto GM, Ferreira ML. Burkholderia cepacia lipase: A versatile catalyst in synthesis reactions. Biotechnol Bioeng 2017;115:6-24. [DOI: 10.1002/bit.26458] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 07/14/2017] [Accepted: 09/21/2017] [Indexed: 12/19/2022]
20
Rasolohery I, Moroy G, Guyon F. PatchSearch: A Fast Computational Method for Off-Target Detection. J Chem Inf Model 2017;57:769-777. [PMID: 28282119 DOI: 10.1021/acs.jcim.6b00529] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
21
Ahmed HR, Glasgow JI. The Agile particle swarm optimizer applied to proteomic pattern matching and discovery. Soft comput 2016. [DOI: 10.1007/s00500-015-1769-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
22
CRHunter: integrating multifaceted information to predict catalytic residues in enzymes. Sci Rep 2016;6:34044. [PMID: 27665935 PMCID: PMC5036049 DOI: 10.1038/srep34044] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 09/07/2016] [Indexed: 11/08/2022]  Open
23
Ruiz-Gómez G, Hawkins JC, Philipp J, Künze G, Wodtke R, Löser R, Fahmy K, Pisabarro MT. Rational Structure-Based Rescaffolding Approach to De Novo Design of Interleukin 10 (IL-10) Receptor-1 Mimetics. PLoS One 2016;11:e0154046. [PMID: 27123592 PMCID: PMC4849758 DOI: 10.1371/journal.pone.0154046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 04/07/2016] [Indexed: 12/25/2022]  Open
24
SÁENZ-SUÁREZ H, POUTOU-PIÑALES RA, GONZÁLEZ-SANTOS J, BARRETO GE, RIETO-NAVARRERA LP, SÁENZ-MORENO JA, LANDÁZURI P, BARRERA-AVELLANEDA LA. Prediction of glycation sites: new insights from protein structural analysis. Turk J Biol 2016. [DOI: 10.3906/biy-1501-71] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]  Open
25
Ramirez-Manzanares A, Peña J, Azpiroz JM, Merino G. A hierarchical algorithm for molecular similarity (H-FORMS). J Comput Chem 2015;36:1456-66. [DOI: 10.1002/jcc.23947] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 04/24/2015] [Accepted: 04/27/2015] [Indexed: 11/10/2022]
26
Abu Seman N, He B, Ojala JRM, Wan Mohamud WN, Östenson CG, Brismar K, Gu HF. Genetic and biological effects of sodium-chloride cotransporter (SLC12A3) in diabetic nephropathy. Am J Nephrol 2014;40:408-16. [PMID: 25401745 DOI: 10.1159/000368916] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 10/06/2014] [Indexed: 11/19/2022]
27
Izidoro SC, de Melo-Minardi RC, Pappa GL. GASS: identifying enzyme active sites with genetic algorithms. ACTA ACUST UNITED AC 2014;31:864-70. [PMID: 25388152 DOI: 10.1093/bioinformatics/btu746] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
28
Flores DI, Sotelo-Mundo RR, Brizuela CA. A simple extension to the CMASA method for the prediction of catalytic residues in the presence of single point mutations. PLoS One 2014;9:e108513. [PMID: 25268770 PMCID: PMC4182483 DOI: 10.1371/journal.pone.0108513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 08/31/2014] [Indexed: 11/23/2022]  Open
29
Brylinski M. eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models. PLoS Comput Biol 2014;10:e1003829. [PMID: 25232727 PMCID: PMC4168975 DOI: 10.1371/journal.pcbi.1003829] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 07/24/2014] [Indexed: 01/26/2023]  Open
30
Micale G, Pulvirenti A, Giugno R, Ferro A. Proteins comparison through probabilistic optimal structure local alignment. Front Genet 2014;5:302. [PMID: 25228906 PMCID: PMC4151033 DOI: 10.3389/fgene.2014.00302] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Accepted: 08/12/2014] [Indexed: 11/13/2022]  Open
31
Oldfield T. Mathematical Data Mining. CRYSTALLOGR REV 2014. [DOI: 10.1080/08893110410001664909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
32
Saberi Fathi SM, Tuszynski JA. A simple method for finding a protein's ligand-binding pockets. BMC STRUCTURAL BIOLOGY 2014;14:18. [PMID: 25038637 PMCID: PMC4112621 DOI: 10.1186/1472-6807-14-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 07/11/2014] [Indexed: 12/03/2022]
33
Steinkellner G, Gruber CC, Pavkov-Keller T, Binter A, Steiner K, Winkler C, Łyskowski A, Schwamberger O, Oberer M, Schwab H, Faber K, Macheroux P, Gruber K. Identification of promiscuous ene-reductase activity by mining structural databases using active site constellations. Nat Commun 2014;5:4150. [PMID: 24954722 PMCID: PMC4083419 DOI: 10.1038/ncomms5150] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 05/15/2014] [Indexed: 12/03/2022]  Open
34
Buturovic L, Wong M, Tang GW, Altman RB, Petkovic D. High precision prediction of functional sites in protein structures. PLoS One 2014;9:e91240. [PMID: 24632601 PMCID: PMC3954699 DOI: 10.1371/journal.pone.0091240] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 02/11/2014] [Indexed: 11/29/2022]  Open
35
Exploiting structural information for drug-target assessment. Future Med Chem 2014;6:319-31. [DOI: 10.4155/fmc.14.3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
36
Rodriguez A, Schmidler SC. BAYESIAN PROTEIN STRUCTURE ALIGNMENT. Ann Appl Stat 2014;8:2068-2095. [PMID: 26925188 DOI: 10.1214/14-aoas780] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
37
Nemoto W, Saito A, Oikawa H. Recent advances in functional region prediction by using structural and evolutionary information - Remaining problems and future extensions. Comput Struct Biotechnol J 2013;8:e201308007. [PMID: 24688747 PMCID: PMC3962155 DOI: 10.5936/csbj.201308007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 11/12/2013] [Accepted: 11/13/2013] [Indexed: 11/22/2022]  Open
38
Caprari S, Toti D, Viet Hung L, Di Stefano M, Polticelli F. ASSIST: a fast versatile local structural comparison tool. Bioinformatics 2013;30:1022-4. [DOI: 10.1093/bioinformatics/btt664] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
39
Prediction and experimental validation of enzyme substrate specificity in protein structures. Proc Natl Acad Sci U S A 2013;110:E4195-202. [PMID: 24145433 DOI: 10.1073/pnas.1305162110] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
40
Jalencas X, Mestres J. Identification of Similar Binding Sites to Detect Distant Polypharmacology. Mol Inform 2013;32:976-90. [PMID: 27481143 DOI: 10.1002/minf.201300082] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 07/29/2013] [Indexed: 01/19/2023]
41
He L, Vandin F, Pandurangan G, Bailey-Kellogg C. Ballast: a ball-based algorithm for structural motifs. J Comput Biol 2013;20:137-51. [PMID: 23383999 DOI: 10.1089/cmb.2012.0246] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
42
Nilmeier JP, Kirshner DA, Wong SE, Lightstone FC. Rapid catalytic template searching as an enzyme function prediction procedure. PLoS One 2013;8:e62535. [PMID: 23675414 PMCID: PMC3651201 DOI: 10.1371/journal.pone.0062535] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 03/22/2013] [Indexed: 11/18/2022]  Open
43
Volkamer A, Kuhn D, Rippmann F, Rarey M. Predicting enzymatic function from global binding site descriptors. Proteins 2012;81:479-89. [DOI: 10.1002/prot.24205] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 09/21/2012] [Accepted: 10/11/2012] [Indexed: 11/09/2022]
44
Ellingson L, Zhang J. Protein surface matching by combining local and global geometric information. PLoS One 2012;7:e40540. [PMID: 22815760 PMCID: PMC3398928 DOI: 10.1371/journal.pone.0040540] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 06/12/2012] [Indexed: 01/01/2023]  Open
45
Wu CY, Hwa YH, Chen YC, Lim C. Hidden relationship between conserved residues and locally conserved phosphate-binding structures in NAD(P)-binding proteins. J Phys Chem B 2012;116:5644-52. [PMID: 22530587 DOI: 10.1021/jp3014332] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
46
Ueno K, Mineta K, Ito K, Endo T. Exploring functionally related enzymes using radially distributed properties of active sites around the reacting points of bound ligands. BMC STRUCTURAL BIOLOGY 2012;12:5. [PMID: 22536854 PMCID: PMC3408369 DOI: 10.1186/1472-6807-12-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Accepted: 04/26/2012] [Indexed: 11/10/2022]
47
Kinjo AR, Nakamura H. Composite structural motifs of binding sites for delineating biological functions of proteins. PLoS One 2012;7:e31437. [PMID: 22347478 PMCID: PMC3275580 DOI: 10.1371/journal.pone.0031437] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 01/08/2012] [Indexed: 11/19/2022]  Open
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Sacan A, Ekins S, Kortagere S. Applications and limitations of in silico models in drug discovery. Methods Mol Biol 2012;910:87-124. [PMID: 22821594 DOI: 10.1007/978-1-61779-965-5_6] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Ming D, Wall ME. Predicting binding sites by analyzing allosteric effects. Methods Mol Biol 2012;796:423-436. [PMID: 22052504 DOI: 10.1007/978-1-61779-334-9_23] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
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Stegemann B, Klebe G. Cofactor-binding sites in proteins of deviating sequence: comparative analysis and clustering in torsion angle, cavity, and fold space. Proteins 2011;80:626-48. [PMID: 22095739 DOI: 10.1002/prot.23226] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 09/29/2011] [Accepted: 10/10/2011] [Indexed: 12/13/2022]
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