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For: Xia Y, Levitt M. Extracting knowledge-based energy functions from protein structures by error rate minimization: Comparison of methods using lattice model. J Chem Phys 2000. [DOI: 10.1063/1.1320823] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
Number Cited by Other Article(s)
1
All-Atom Four-Body Knowledge-Based Statistical Potentials to Distinguish Native Protein Structures from Nonnative Folds. BIOMED RESEARCH INTERNATIONAL 2017;2017:5760612. [PMID: 29119109 PMCID: PMC5651141 DOI: 10.1155/2017/5760612] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/13/2017] [Accepted: 08/23/2017] [Indexed: 02/05/2023]
2
Kmiecik S, Gront D, Kolinski M, Wieteska L, Dawid AE, Kolinski A. Coarse-Grained Protein Models and Their Applications. Chem Rev 2016;116:7898-936. [DOI: 10.1021/acs.chemrev.6b00163] [Citation(s) in RCA: 555] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
3
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]
4
Zhang J, Chen R, Liang J. Potential function of simplified protein models for discriminating native proteins from decoys: combining contact interaction and local sequence-dependent geometry. CONFERENCE PROCEEDINGS : ... ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL CONFERENCE 2007;2004:2976-9. [PMID: 17270903 DOI: 10.1109/iembs.2004.1403844] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
5
Zhang J, Chen R, Liang J. Empirical potential function for simplified protein models: combining contact and local sequence-structure descriptors. Proteins 2006;63:949-60. [PMID: 16477624 DOI: 10.1002/prot.20809] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
6
Li X, Liang J. Geometric cooperativity and anticooperativity of three-body interactions in native proteins. Proteins 2005;60:46-65. [PMID: 15849756 DOI: 10.1002/prot.20438] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
7
Kolinski A, Skolnick J. Reduced models of proteins and their applications. POLYMER 2004. [DOI: 10.1016/j.polymer.2003.10.064] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
8
Optimization of protein force-field parameters with the Protein Data Bank. Chem Phys Lett 2003. [DOI: 10.1016/j.cplett.2003.10.107] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
9
Li X, Hu C, Liang J. Simplicial edge representation of protein structures and alpha contact potential with confidence measure. Proteins 2003;53:792-805. [PMID: 14635122 DOI: 10.1002/prot.10442] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
10
Eastwood MP, Hardin C, Luthey-Schulten Z, Wolynes PG. Statistical mechanical refinement of protein structure prediction schemes. II. Mayer cluster expansion approach. J Chem Phys 2003. [DOI: 10.1063/1.1565106] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]  Open
11
McConkey BJ, Sobolev V, Edelman M. Discrimination of native protein structures using atom-atom contact scoring. Proc Natl Acad Sci U S A 2003;100:3215-20. [PMID: 12631702 PMCID: PMC152272 DOI: 10.1073/pnas.0535768100] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
12
Eastwood MP, Hardin C, Luthey-Schulten Z, Wolynes PG. Statistical mechanical refinement of protein structure prediction schemes: Cumulant expansion approach. J Chem Phys 2002. [DOI: 10.1063/1.1494417] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]  Open
13
Fain B, Xia Y, Levitt M. Design of an optimal Chebyshev-expanded discrimination function for globular proteins. Protein Sci 2002;11:2010-21. [PMID: 12142455 PMCID: PMC2373672 DOI: 10.1110/ps.0200702] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
14
Russell AJ, Torda AE. Protein sequence threading: Averaging over structures. Proteins 2002;47:496-505. [PMID: 12001228 DOI: 10.1002/prot.10088] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
15
Vendruscolo M. Energetics of enzyme stability. Trends Biotechnol 2002;20:1-2; discussion 2-3. [PMID: 11742663 DOI: 10.1016/s0167-7799(01)01871-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
16
Bastolla U, Farwer J, Knapp EW, Vendruscolo M. How to guarantee optimal stability for most representative structures in the Protein Data Bank. Proteins 2001;44:79-96. [PMID: 11391771 DOI: 10.1002/prot.1075] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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