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For: Samudrala R, Moult J. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J Mol Biol 1998;275:895-916. [PMID: 9480776 DOI: 10.1006/jmbi.1997.1479] [Citation(s) in RCA: 325] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Number Cited by Other Article(s)
101
Basu S, Bhattacharyya D, Banerjee R. Self-complementarity within proteins: bridging the gap between binding and folding. Biophys J 2012;102:2605-14. [PMID: 22713576 DOI: 10.1016/j.bpj.2012.04.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 03/30/2012] [Accepted: 04/17/2012] [Indexed: 01/09/2023]  Open
102
Ceres N, Lavery R. Coarse-grain Protein Models. INNOVATIONS IN BIOMOLECULAR MODELING AND SIMULATIONS 2012. [DOI: 10.1039/9781849735049-00219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
103
Zimmermann MT, Leelananda SP, Kloczkowski A, Jernigan RL. Combining statistical potentials with dynamics-based entropies improves selection from protein decoys and docking poses. J Phys Chem B 2012;116:6725-31. [PMID: 22490366 DOI: 10.1021/jp2120143] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
104
Fan H, Periole X, Mark AE. Mimicking the action of folding chaperones by Hamiltonian replica-exchange molecular dynamics simulations: application in the refinement of de novo models. Proteins 2012;80:1744-54. [PMID: 22411697 DOI: 10.1002/prot.24068] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Revised: 02/11/2012] [Accepted: 03/03/2012] [Indexed: 12/25/2022]
105
Cossio P, Granata D, Laio A, Seno F, Trovato A. A simple and efficient statistical potential for scoring ensembles of protein structures. Sci Rep 2012. [DOI: 10.1038/srep00351] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]  Open
106
Gront D, Kmiecik S, Blaszczyk M, Ekonomiuk D, Koliński A. Optimization of protein models. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1090] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
107
Zhou H, Skolnick J. GOAP: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction. Biophys J 2012;101:2043-52. [PMID: 22004759 DOI: 10.1016/j.bpj.2011.09.012] [Citation(s) in RCA: 201] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Revised: 09/07/2011] [Accepted: 09/09/2011] [Indexed: 12/18/2022]  Open
108
Mirzaie M, Sadeghi M. Distance-dependent atomic knowledge-based force in protein fold recognition. Proteins 2012;80:683-90. [DOI: 10.1002/prot.24011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Revised: 11/15/2011] [Accepted: 12/06/2011] [Indexed: 11/08/2022]
109
Masso M. Generation of atomic four-body statistical potentials derived from the delaunay tessellation of protein structures. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2012;2012:6321-6324. [PMID: 23367374 DOI: 10.1109/embc.2012.6347439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
110
Li H, Zhou Y. FOLD HELICAL PROTEINS BY ENERGY MINIMIZATION IN DIHEDRAL SPACE AND A DFIRE-BASED STATISTICAL ENERGY FUNCTION. J Bioinform Comput Biol 2011;3:1151-70. [PMID: 16278952 DOI: 10.1142/s0219720005001430] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2004] [Revised: 04/12/2005] [Accepted: 04/21/2005] [Indexed: 11/18/2022]
111
Fan H, Schneidman-Duhovny D, Irwin JJ, Dong G, Shoichet BK, Sali A. Statistical potential for modeling and ranking of protein-ligand interactions. J Chem Inf Model 2011;51:3078-92. [PMID: 22014038 DOI: 10.1021/ci200377u] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
112
SAKAE YOSHITAKE, OKAMOTO YUKO. PROTEIN FORCE-FIELD PARAMETERS OPTIMIZED WITH THE PROTEIN DATA BANK I: FORCE-FIELD OPTIMIZATIONS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633604001082] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
113
Wang Q, Shang Y, Xu D. Improving a consensus approach for protein structure selection by removing redundancy. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2011;8:1708-15. [PMID: 21519117 DOI: 10.1109/tcbb.2011.75] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
114
Choi Y, Deane CM. Predicting antibody complementarity determining region structures without classification. MOLECULAR BIOSYSTEMS 2011;7:3327-34. [PMID: 22011953 DOI: 10.1039/c1mb05223c] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
115
Zhang J, Wang Q, Vantasin K, Zhang J, He Z, Kosztin I, Shang Y, Xu D. A multilayer evaluation approach for protein structure prediction and model quality assessment. Proteins 2011;79 Suppl 10:172-84. [PMID: 21997706 DOI: 10.1002/prot.23184] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 08/26/2011] [Accepted: 09/05/2011] [Indexed: 01/03/2023]
116
Zhou W, Yan H. Prediction of DNA-binding protein based on statistical and geometric features and support vector machines. Proteome Sci 2011;9 Suppl 1:S1. [PMID: 22166014 PMCID: PMC3289070 DOI: 10.1186/1477-5956-9-s1-s1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]  Open
117
Wang Q, Vantasin K, Xu D, Shang Y. MUFOLD-WQA: A new selective consensus method for quality assessment in protein structure prediction. Proteins 2011;79 Suppl 10:185-95. [PMID: 21997748 DOI: 10.1002/prot.23185] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 08/25/2011] [Accepted: 08/27/2011] [Indexed: 11/07/2022]
118
Wainreb G, Wolf L, Ashkenazy H, Dehouck Y, Ben-Tal N. Protein stability: a single recorded mutation aids in predicting the effects of other mutations in the same amino acid site. ACTA ACUST UNITED AC 2011;27:3286-92. [PMID: 21998155 PMCID: PMC3223369 DOI: 10.1093/bioinformatics/btr576] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
119
Hu C, Koehl P, Max N. PackHelix: a tool for helix-sheet packing during protein structure prediction. Proteins 2011;79:2828-43. [PMID: 21905109 PMCID: PMC3172692 DOI: 10.1002/prot.23108] [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: 02/02/2011] [Revised: 04/18/2011] [Accepted: 05/13/2011] [Indexed: 11/09/2022]
120
Moughon SE, Samudrala R. LoCo: a novel main chain scoring function for protein structure prediction based on local coordinates. BMC Bioinformatics 2011;12:368. [PMID: 21920038 PMCID: PMC3184297 DOI: 10.1186/1471-2105-12-368] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 09/15/2011] [Indexed: 11/10/2022]  Open
121
Lertkiatmongkol P, Jenwitheesuk E, Rongnoparut P. Homology modeling of mosquito cytochrome P450 enzymes involved in pyrethroid metabolism: insights into differences in substrate selectivity. BMC Res Notes 2011;4:321. [PMID: 21892968 PMCID: PMC3228512 DOI: 10.1186/1756-0500-4-321] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 09/06/2011] [Indexed: 11/29/2022]  Open
122
Shi X, Zhang J, He Z, Shang Y, Xu D. A sampling-based method for ranking protein structural models by integrating multiple scores and features. Curr Protein Pept Sci 2011;12:540-8. [PMID: 21787308 PMCID: PMC4368063 DOI: 10.2174/138920311796957658] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 04/01/2011] [Accepted: 05/04/2011] [Indexed: 11/22/2022]
123
Liu S, Vakser IA. DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking. BMC Bioinformatics 2011;12:280. [PMID: 21745398 PMCID: PMC3145612 DOI: 10.1186/1471-2105-12-280] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Accepted: 07/11/2011] [Indexed: 11/13/2022]  Open
124
Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models. ACTA ACUST UNITED AC 2011;12:137-47. [PMID: 21674234 DOI: 10.1007/s10969-011-9113-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2010] [Accepted: 05/26/2011] [Indexed: 01/02/2023]
125
Ghasemi JB, Salahinejad M, Rofouei MK. Review of the quantitative structure–activity relationship modelling methods on estimation of formation constants of macrocyclic compounds with different guest molecules. Supramol Chem 2011. [DOI: 10.1080/10610278.2011.581281] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
126
Bernauer J, Huang X, Sim AYL, Levitt M. Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation. RNA (NEW YORK, N.Y.) 2011;17:1066-1075. [PMID: 21521828 PMCID: PMC3096039 DOI: 10.1261/rna.2543711] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 03/01/2011] [Indexed: 05/27/2023]
127
Tian L, Wu A, Cao Y, Dong X, Hu Y, Jiang T. NCACO-score: an effective main-chain dependent scoring function for structure modeling. BMC Bioinformatics 2011;12:208. [PMID: 21612673 PMCID: PMC3123610 DOI: 10.1186/1471-2105-12-208] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 05/26/2011] [Indexed: 11/10/2022]  Open
128
Cunningham ML, Horst JA, Rieder MJ, Hing AV, Stanaway IB, Park SS, Samudrala R, Speltz ML. IGF1R variants associated with isolated single suture craniosynostosis. Am J Med Genet A 2011;155A:91-7. [PMID: 21204214 DOI: 10.1002/ajmg.a.33781] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
129
Liang S, Zhang C, Standley DM. Protein loop selection using orientation-dependent force fields derived by parameter optimization. Proteins 2011;79:2260-7. [DOI: 10.1002/prot.23051] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 03/21/2011] [Accepted: 03/31/2011] [Indexed: 12/25/2022]
130
Sun W, He J. From isotropic to anisotropic side chain representations: comparison of three models for residue contact estimation. PLoS One 2011;6:e19238. [PMID: 21552527 PMCID: PMC3084275 DOI: 10.1371/journal.pone.0019238] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Accepted: 03/29/2011] [Indexed: 11/19/2022]  Open
131
Gniewek P, Leelananda SP, Kolinski A, Jernigan RL, Kloczkowski A. Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models. Proteins 2011;79:1923-9. [PMID: 21560165 DOI: 10.1002/prot.23015] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Revised: 01/07/2011] [Accepted: 01/28/2011] [Indexed: 01/02/2023]
132
Shirota M, Ishida T, Kinoshita K. Absolute quality evaluation of protein model structures using statistical potentials with respect to the native and reference states. Proteins 2011;79:1550-63. [PMID: 21365682 DOI: 10.1002/prot.22982] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2010] [Revised: 11/19/2010] [Accepted: 12/19/2010] [Indexed: 11/06/2022]
133
Dong Q, Zhou S. Novel nonlinear knowledge-based mean force potentials based on machine learning. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2011;8:476-486. [PMID: 20820079 DOI: 10.1109/tcbb.2010.86] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
134
Adamczak R, Pillardy J, Vallat BK, Meller J. Fast geometric consensus approach for protein model quality assessment. J Comput Biol 2011;18:1807-18. [PMID: 21244273 DOI: 10.1089/cmb.2010.0170] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
135
Totrov M. Loop simulations. Methods Mol Biol 2011;857:207-29. [PMID: 22323223 DOI: 10.1007/978-1-61779-588-6_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
136
Zhou Y, Duan Y, Yang Y, Faraggi E, Lei H. Trends in template/fragment-free protein structure prediction. Theor Chem Acc 2011;128:3-16. [PMID: 21423322 PMCID: PMC3030773 DOI: 10.1007/s00214-010-0799-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 08/15/2010] [Indexed: 12/13/2022]
137
Benkert P, Biasini M, Schwede T. Toward the estimation of the absolute quality of individual protein structure models. ACTA ACUST UNITED AC 2010;27:343-50. [PMID: 21134891 PMCID: PMC3031035 DOI: 10.1093/bioinformatics/btq662] [Citation(s) in RCA: 1517] [Impact Index Per Article: 108.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
138
Hamelryck T, Borg M, Paluszewski M, Paulsen J, Frellsen J, Andreetta C, Boomsma W, Bottaro S, Ferkinghoff-Borg J. Potentials of mean force for protein structure prediction vindicated, formalized and generalized. PLoS One 2010;5:e13714. [PMID: 21103041 PMCID: PMC2978081 DOI: 10.1371/journal.pone.0013714] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Accepted: 10/04/2010] [Indexed: 11/26/2022]  Open
139
Zhang J, Zhang Y. A novel side-chain orientation dependent potential derived from random-walk reference state for protein fold selection and structure prediction. PLoS One 2010;5:e15386. [PMID: 21060880 PMCID: PMC2965178 DOI: 10.1371/journal.pone.0015386] [Citation(s) in RCA: 171] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Accepted: 09/01/2010] [Indexed: 11/18/2022]  Open
140
Ray A, Lindahl E, Wallner B. Model quality assessment for membrane proteins. Bioinformatics 2010;26:3067-74. [DOI: 10.1093/bioinformatics/btq581] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
141
Tian Y, Deutsch C, Krishnamoorthy B. Scoring function to predict solubility mutagenesis. Algorithms Mol Biol 2010;5:33. [PMID: 20929563 PMCID: PMC2958853 DOI: 10.1186/1748-7188-5-33] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Accepted: 10/07/2010] [Indexed: 11/16/2022]  Open
142
Zhou W, Yan H. A discriminatory function for prediction of protein-DNA interactions based on alpha shape modeling. Bioinformatics 2010;26:2541-8. [DOI: 10.1093/bioinformatics/btq478] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
143
Dibble CF, Horst JA, Malone MH, Park K, Temple B, Cheeseman H, Barbaro JR, Johnson GL, Bencharit S. Defining the functional domain of programmed cell death 10 through its interactions with phosphatidylinositol-3,4,5-trisphosphate. PLoS One 2010;5:e11740. [PMID: 20668527 PMCID: PMC2909203 DOI: 10.1371/journal.pone.0011740] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 07/01/2010] [Indexed: 11/25/2022]  Open
144
Potapov V, Cohen M, Inbar Y, Schreiber G. Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions. BMC Bioinformatics 2010;11:374. [PMID: 20624289 PMCID: PMC2912888 DOI: 10.1186/1471-2105-11-374] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Accepted: 07/12/2010] [Indexed: 11/11/2022]  Open
145
Costin JM, Jenwitheesuk E, Lok SM, Hunsperger E, Conrads KA, Fontaine KA, Rees CR, Rossmann MG, Isern S, Samudrala R, Michael SF. Structural optimization and de novo design of dengue virus entry inhibitory peptides. PLoS Negl Trop Dis 2010;4:e721. [PMID: 20582308 PMCID: PMC2889824 DOI: 10.1371/journal.pntd.0000721] [Citation(s) in RCA: 79] [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: 09/11/2009] [Accepted: 04/29/2010] [Indexed: 01/15/2023]  Open
146
Choi Y, Deane CM. FREAD revisited: Accurate loop structure prediction using a database search algorithm. Proteins 2010;78:1431-40. [PMID: 20034110 DOI: 10.1002/prot.22658] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
147
Distance-dependent statistical potentials for discriminating thermophilic and mesophilic proteins. Biochem Biophys Res Commun 2010;396:736-41. [PMID: 20451495 DOI: 10.1016/j.bbrc.2010.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Accepted: 05/02/2010] [Indexed: 11/22/2022]
148
Zhang J, Wang Q, Barz B, He Z, Kosztin I, Shang Y, Xu D. MUFOLD: A new solution for protein 3D structure prediction. Proteins 2010;78:1137-52. [PMID: 19927325 DOI: 10.1002/prot.22634] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
149
Bordner AJ. Orientation-dependent backbone-only residue pair scoring functions for fixed backbone protein design. BMC Bioinformatics 2010;11:192. [PMID: 20398384 PMCID: PMC2874805 DOI: 10.1186/1471-2105-11-192] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Accepted: 04/16/2010] [Indexed: 11/24/2022]  Open
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Rykunov D, Fiser A. New statistical potential for quality assessment of protein models and a survey of energy functions. BMC Bioinformatics 2010;11:128. [PMID: 20226048 PMCID: PMC2853469 DOI: 10.1186/1471-2105-11-128] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Accepted: 03/12/2010] [Indexed: 11/30/2022]  Open
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