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For: Dokholyan NV. What is the protein design alphabet? Proteins 2004;54:622-8. [PMID: 14997558 DOI: 10.1002/prot.10633] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Number Cited by Other Article(s)
1
Magi Meconi G, Sasselli IR, Bianco V, Onuchic JN, Coluzza I. Key aspects of the past 30 years of protein design. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2022;85:086601. [PMID: 35704983 DOI: 10.1088/1361-6633/ac78ef] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
2
Dokholyan NV. Controlling Allosteric Networks in Proteins. Chem Rev 2016;116:6463-87. [PMID: 26894745 DOI: 10.1021/acs.chemrev.5b00544] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
3
Ferreira DC, van der Linden MG, de Oliveira LC, Onuchic JN, de Araújo AFP. Information and redundancy in the burial folding code of globular proteins within a wide range of shapes and sizes. Proteins 2016;84:515-31. [PMID: 26815167 DOI: 10.1002/prot.24998] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 12/28/2015] [Accepted: 01/19/2016] [Indexed: 11/09/2022]
4
Proctor EA, Ding F, Dokholyan NV. Discrete molecular dynamics. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.4] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
5
Randić M, Zupan J, Balaban AT, Vikić-Topić D, Plavšić D. Graphical Representation of Proteins. Chem Rev 2010;111:790-862. [PMID: 20939561 DOI: 10.1021/cr800198j] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
6
A sequence-compatible amount of native burial information is sufficient for determining the structure of small globular proteins. Proc Natl Acad Sci U S A 2009;106:19001-4. [PMID: 19858496 DOI: 10.1073/pnas.0910851106] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
7
Lai Z, Su J, Chen W, Wang C. Uncovering the properties of energy-weighted conformation space networks with a hydrophobic-hydrophilic model. Int J Mol Sci 2009;10:1808-1823. [PMID: 19468340 PMCID: PMC2680648 DOI: 10.3390/ijms10041808] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Revised: 03/30/2009] [Accepted: 04/07/2009] [Indexed: 11/16/2022]  Open
8
Etchebest C, Benros C, Bornot A, Camproux AC, de Brevern AG. A reduced amino acid alphabet for understanding and designing protein adaptation to mutation. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007;36:1059-69. [PMID: 17565494 DOI: 10.1007/s00249-007-0188-5] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2007] [Revised: 05/05/2007] [Accepted: 05/07/2007] [Indexed: 10/23/2022]
9
Khatun J, Khare SD, Dokholyan NV. Can Contact Potentials Reliably Predict Stability of Proteins? J Mol Biol 2004;336:1223-38. [PMID: 15037081 DOI: 10.1016/j.jmb.2004.01.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2003] [Revised: 01/08/2004] [Accepted: 01/08/2004] [Indexed: 11/17/2022]
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