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For: Handl J, Knowles J, Lovell SC. Artefacts and biases affecting the evaluation of scoring functions on decoy sets for protein structure prediction. Bioinformatics 2009;25:1271-9. [PMID: 19297350 PMCID: PMC2677743 DOI: 10.1093/bioinformatics/btp150] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Revised: 03/06/2009] [Accepted: 03/14/2009] [Indexed: 11/15/2022]  Open
Number Cited by Other Article(s)
1
Wang X, Huang SY. Integrating Bonded and Nonbonded Potentials in the Knowledge-Based Scoring Function for Protein Structure Prediction. J Chem Inf Model 2019;59:3080-3090. [DOI: 10.1021/acs.jcim.9b00057] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
2
Colbes J, Corona RI, Lezcano C, Rodríguez D, Brizuela CA. Protein side-chain packing problem: is there still room for improvement? Brief Bioinform 2018;18:1033-1043. [PMID: 27567382 DOI: 10.1093/bib/bbw079] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Indexed: 11/12/2022]  Open
3
Anishchenko I, Kundrotas PJ, Vakser IA. Contact Potential for Structure Prediction of Proteins and Protein Complexes from Potts Model. Biophys J 2018;115:809-821. [PMID: 30122295 DOI: 10.1016/j.bpj.2018.07.035] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 07/16/2018] [Accepted: 07/31/2018] [Indexed: 12/18/2022]  Open
4
Deng H, Jia Y, Zhang Y. 3DRobot: automated generation of diverse and well-packed protein structure decoys. Bioinformatics 2015;32:378-87. [PMID: 26471454 DOI: 10.1093/bioinformatics/btv601] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 10/10/2015] [Indexed: 11/12/2022]  Open
5
Yeh HYC, Lindsey A, Wu CP, Thomas S, Amato NM. Decoy Database Improvement for Protein Folding. J Comput Biol 2015;22:823-36. [PMID: 26258648 DOI: 10.1089/cmb.2015.0116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
6
Wang J, Zhao Y, Zhu C, Xiao Y. 3dRNAscore: a distance and torsion angle dependent evaluation function of 3D RNA structures. Nucleic Acids Res 2015;43:e63. [PMID: 25712091 PMCID: PMC4446410 DOI: 10.1093/nar/gkv141] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 02/06/2015] [Indexed: 01/02/2023]  Open
7
Carlsen M, Koehl P, Røgen P. On the importance of the distance measures used to train and test knowledge-based potentials for proteins. PLoS One 2014;9:e109335. [PMID: 25411785 PMCID: PMC4239004 DOI: 10.1371/journal.pone.0109335] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Accepted: 08/31/2014] [Indexed: 12/15/2022]  Open
8
Ruiz-Blanco YB, Marrero-Ponce Y, García Y, Puris A, Bello R, Green J, Sotomayor-Torres CM. A physics-based scoring function for protein structural decoys: Dynamic testing on targets of CASP-ROLL. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.07.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
9
Chakraborty S, Venkatramani R, Rao BJ, Asgeirsson B, Dandekar AM. The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment. F1000Res 2013;2:243. [PMID: 25506420 PMCID: PMC4257144 DOI: 10.12688/f1000research.2-243.v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/16/2014] [Indexed: 02/10/2024]  Open
10
Chakraborty S, Venkatramani R, Rao BJ, Asgeirsson B, Dandekar AM. Protein structure quality assessment based on the distance profiles of consecutive backbone Cα atoms. F1000Res 2013;2:211. [PMID: 24555103 PMCID: PMC3892923 DOI: 10.12688/f1000research.2-211.v1#sthash.lfll9fko.snt845h1.dpuf] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/16/2013] [Indexed: 06/29/2024]  Open
11
Chakraborty S, Venkatramani R, Rao BJ, Asgeirsson B, Dandekar AM. Protein structure quality assessment based on the distance profiles of consecutive backbone Cα atoms. F1000Res 2013;2:211. [PMID: 24555103 DOI: 10.12688/f1000research.2-211.v1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/10/2013] [Indexed: 01/22/2023]  Open
12
Kauffman C, Karypis G. Coarse- and fine-grained models for proteins: Evaluation by decoy discrimination. Proteins 2013. [DOI: 10.1002/prot.24222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
13
Chakraborty S, Venkatramani R, Rao BJ, Asgeirsson B, Dandekar AM. The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment. F1000Res 2013;2:243. [PMID: 25506420 PMCID: PMC4257144 DOI: 10.12688/f1000research.2-243.v3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/16/2014] [Indexed: 12/23/2022]  Open
14
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: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]  Open
15
Developing a high-quality scoring function for membrane protein structures based on specific inter-residue interactions. J Comput Aided Mol Des 2012;26:301-9. [PMID: 22395902 DOI: 10.1007/s10822-012-9556-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 02/19/2012] [Indexed: 10/28/2022]
16
Huang SY, Zou X. Statistical mechanics-based method to extract atomic distance-dependent potentials from protein structures. Proteins 2011;79:2648-61. [PMID: 21732421 PMCID: PMC11108592 DOI: 10.1002/prot.23086] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2011] [Revised: 04/21/2011] [Accepted: 05/09/2011] [Indexed: 12/25/2022]
17
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: 66] [Impact Index Per Article: 4.7] [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]
18
Kalman M, Ben-Tal N. Quality assessment of protein model-structures using evolutionary conservation. ACTA ACUST UNITED AC 2010;26:1299-307. [PMID: 20385730 PMCID: PMC2865859 DOI: 10.1093/bioinformatics/btq114] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
19
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: 4.8] [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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