메뉴 건너뛰기




Volumn 25, Issue 1, 2016, Pages 111-122

Constructing sequence-dependent protein models using coevolutionary information

Author keywords

coarse grained protein models; coevolutionary information; computational biophysics; statistical inference

Indexed keywords

PROTEIN S6; PROTEIN SH3; PROTEIN;

EID: 84959183728     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.2758     Document Type: Article
Times cited : (15)

References (72)
  • 1
    • 0023449962 scopus 로고
    • Spin-glasses and the statistical-mechanics of protein folding
    • Bryngelson JD, Wolynes PG, (1987) Spin-glasses and the statistical-mechanics of protein folding. Proc Natl Acad Sci USA 84: 7524-7528.
    • (1987) Proc Natl Acad Sci USA , vol.84 , pp. 7524-7528
    • Bryngelson, J.D.1    Wolynes, P.G.2
  • 4
    • 63449135082 scopus 로고    scopus 로고
    • An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical force fields
    • Whitford PC, Noel JK, Gosavi S, Schug A, Sanbonmatsu KY, Onuchic JN, (2009) An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical force fields. Proteins 75: 430-441.
    • (2009) Proteins , vol.75 , pp. 430-441
    • Whitford, P.C.1    Noel, J.K.2    Gosavi, S.3    Schug, A.4    Sanbonmatsu, K.Y.5    Onuchic, J.N.6
  • 6
    • 0034685604 scopus 로고    scopus 로고
    • Topological and energetic factors: What determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins
    • Clementi C, Nymeyer H, Onuchic JN, (2000) Topological and energetic factors: What determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins. J Mol Biol 298: 937-953.
    • (2000) J Mol Biol , vol.298 , pp. 937-953
    • Clementi, C.1    Nymeyer, H.2    Onuchic, J.N.3
  • 7
    • 84863522650 scopus 로고    scopus 로고
    • Biomolecular dynamics: Order-disorder transitions and energy landscapes
    • Whitford PC, Sanbonmatsu KY, Onuchic JN, (2012) Biomolecular dynamics: order-disorder transitions and energy landscapes. Rep Prog Phys 75: 076601
    • (2012) Rep Prog Phys , vol.75 , pp. 076601
    • Whitford, P.C.1    Sanbonmatsu, K.Y.2    Onuchic, J.N.3
  • 8
    • 0000197372 scopus 로고    scopus 로고
    • Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
    • Tirion MM, (1996) Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys Rev Lett 77: 1905-1908.
    • (1996) Phys Rev Lett , vol.77 , pp. 1905-1908
    • Tirion, M.M.1
  • 9
    • 0000019986 scopus 로고
    • Protein folding as a stochastic-process
    • Go N, (1983) Protein folding as a stochastic-process. J Statistical Phys 30: 413-423.
    • (1983) J Statistical Phys , vol.30 , pp. 413-423
    • Go, N.1
  • 10
    • 84919770982 scopus 로고    scopus 로고
    • Theoretical perspectives on nonnative interactions and intrinsic disorder in protein folding and binding
    • Chen T, Song JH, Chan HS, (2015) Theoretical perspectives on nonnative interactions and intrinsic disorder in protein folding and binding. Curr Opin Struct Biol 30: 32-42.
    • (2015) Curr Opin Struct Biol , vol.30 , pp. 32-42
    • Chen, T.1    Song, J.H.2    Chan, H.S.3
  • 11
    • 84864213700 scopus 로고    scopus 로고
    • AWSEM-MD: Protein structure prediction using coarse-grained physical potentials and bioinformatically based local structure biasing
    • Davtyan A, Schafer NP, Zheng WH, Clementi C, Wolynes PG, Papoian GA, (2012) AWSEM-MD: Protein structure prediction using coarse-grained physical potentials and bioinformatically based local structure biasing. J Phys Chem B 116: 8494-8503.
    • (2012) J Phys Chem B , vol.116 , pp. 8494-8503
    • Davtyan, A.1    Schafer, N.P.2    Zheng, W.H.3    Clementi, C.4    Wolynes, P.G.5    Papoian, G.A.6
  • 12
    • 84979042804 scopus 로고    scopus 로고
    • Learning to fold proteins using energy landscape theory
    • Schafer NP, Kim BL, Zheng WH, Wolynes PG, (2014) Learning to fold proteins using energy landscape theory. Israel J Chem 54: 1311-1337.
    • (2014) Israel J Chem , vol.54 , pp. 1311-1337
    • Schafer, N.P.1    Kim, B.L.2    Zheng, W.H.3    Wolynes, P.G.4
  • 13
    • 84904968329 scopus 로고    scopus 로고
    • Predictive energy landscapes for folding alpha-helical transmembrane proteins
    • Kim BL, Schafer NP, Wolynes PG, (2014) Predictive energy landscapes for folding alpha-helical transmembrane proteins. Proc Natl Acad Sci USA 111: 11031-11036.
    • (2014) Proc Natl Acad Sci USA , vol.111 , pp. 11031-11036
    • Kim, B.L.1    Schafer, N.P.2    Wolynes, P.G.3
  • 15
    • 4644340168 scopus 로고    scopus 로고
    • Optimal combination of theory and experiment for the characterization of the protein folding landscape of S6: How far can a minimalist model go?
    • Matysiak S, Clementi C, (2004) Optimal combination of theory and experiment for the characterization of the protein folding landscape of S6: How far can a minimalist model go?. J Mol Biol 343: 235-248.
    • (2004) J Mol Biol , vol.343 , pp. 235-248
    • Matysiak, S.1    Clementi, C.2
  • 16
    • 79952774013 scopus 로고    scopus 로고
    • Frustration, specific sequence dependence, and nonlinearity in large-amplitude fluctuations of allosteric proteins
    • Li WF, Wolynes PG, Takada S, (2011) Frustration, specific sequence dependence, and nonlinearity in large-amplitude fluctuations of allosteric proteins. Proc Natl Acad Sci USA 108: 3504-3509.
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 3504-3509
    • Li, W.F.1    Wolynes, P.G.2    Takada, S.3
  • 17
    • 84875225476 scopus 로고    scopus 로고
    • Emerging methods in protein co-evolution
    • de Juan D, Pazos F, Valencia A, (2013) Emerging methods in protein co-evolution. Nature Rev Genet 14: 249-261.
    • (2013) Nature Rev Genet , vol.14 , pp. 249-261
    • De Juan, D.1    Pazos, F.2    Valencia, A.3
  • 18
    • 84869447010 scopus 로고    scopus 로고
    • Protein structure prediction from sequence variation
    • Marks DS, Hopf TA, Sander C, (2012) Protein structure prediction from sequence variation. Nature Biotech 30: 1072-1080.
    • (2012) Nature Biotech , vol.30 , pp. 1072-1080
    • Marks, D.S.1    Hopf, T.A.2    Sander, C.3
  • 19
    • 84866913347 scopus 로고    scopus 로고
    • Correlated electrostatic mutations provide a reservoir of stability in HIV protease
    • Haq O, Andrec M, Morozov AV, Levy RM, (2012) Correlated electrostatic mutations provide a reservoir of stability in HIV protease. Plos Comput Biol 012; 8.
    • (2012) Plos Comput Biol , vol.12 , pp. 8
    • Haq, O.1    Andrec, M.2    Morozov, A.V.3    Levy, R.M.4
  • 20
    • 69549116664 scopus 로고    scopus 로고
    • Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease
    • Haq O, Levy RM, Morozov AV, Andrec M, (2009) Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease. BMC Bioinform 10:
    • (2009) BMC Bioinform , vol.10
    • Haq, O.1    Levy, R.M.2    Morozov, A.V.3    Andrec, M.4
  • 21
    • 84875546274 scopus 로고    scopus 로고
    • Translating HIV sequences into quantitative fitness landscapes predicts viral vulnerabilities for rational immunogen design
    • Ferguson AL, Mann JK, Omarjee S, Ndung'u T, Walker BD, Chakraborty AK, (2013) Translating HIV sequences into quantitative fitness landscapes predicts viral vulnerabilities for rational immunogen design. Immunity 38: 606-617.
    • (2013) Immunity , vol.38 , pp. 606-617
    • Ferguson, A.L.1    Mann, J.K.2    Omarjee, S.3    Ndung'u, T.4    Walker, B.D.5    Chakraborty, A.K.6
  • 22
    • 33646170322 scopus 로고    scopus 로고
    • Weak pairwise correlations imply strongly correlated network states in a neural population
    • Schneidman E, Berry MJ, Segev R, Bialek W, (2006) Weak pairwise correlations imply strongly correlated network states in a neural population. Nature 440: 1007-1012.
    • (2006) Nature , vol.440 , pp. 1007-1012
    • Schneidman, E.1    Berry, M.J.2    Segev, R.3    Bialek, W.4
  • 24
    • 84893476565 scopus 로고    scopus 로고
    • Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information
    • Cheng RR, Morcos F, Levine H, Onuchic JN, (2014) Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information. Proc Natl Acad Sci USA 111: E563-E571.
    • (2014) Proc Natl Acad Sci USA , vol.111 , pp. E563-E571
    • Cheng, R.R.1    Morcos, F.2    Levine, H.3    Onuchic, J.N.4
  • 25
    • 84863006375 scopus 로고    scopus 로고
    • Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis
    • Dago AE, Schug A, Procaccini A, Hoch JA, Weigt M, Szurmant H, (2012) Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis. Proc Natl Acad Sci USA 109: E1733-E1742.
    • (2012) Proc Natl Acad Sci USA , vol.109 , pp. E1733-E1742
    • Dago, A.E.1    Schug, A.2    Procaccini, A.3    Hoch, J.A.4    Weigt, M.5    Szurmant, H.6
  • 26
    • 79955792165 scopus 로고    scopus 로고
    • Dissecting the specificity of protein-protein interaction in bacterial two-component signaling: Orphans and crosstalks
    • Procaccini A, Lunt B, Szurmant H, Hwa T, Weigt M, (2011) Dissecting the specificity of protein-protein interaction in bacterial two-component signaling: orphans and crosstalks. Plos One 6:
    • (2011) Plos One , vol.6
    • Procaccini, A.1    Lunt, B.2    Szurmant, H.3    Hwa, T.4    Weigt, M.5
  • 27
    • 58549114185 scopus 로고    scopus 로고
    • Identification of direct residue contacts in protein-protein interaction by message passing
    • Weigt M, White RA, Szurmant H, Hoch JA, Hwa T, (2009) Identification of direct residue contacts in protein-protein interaction by message passing. Proc Natl Acad Sci USA 106: 67-72.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 67-72
    • Weigt, M.1    White, R.A.2    Szurmant, H.3    Hoch, J.A.4    Hwa, T.5
  • 28
    • 76049105937 scopus 로고    scopus 로고
    • High-resolution protein complexes from integrating genomic information with molecular simulation
    • Schug A, Weigt M, Onuchic JN, Hwa T, Szurmant H, (2009) High-resolution protein complexes from integrating genomic information with molecular simulation. Proc Natl Acad Sci USA 106: 22124-22129.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 22124-22129
    • Schug, A.1    Weigt, M.2    Onuchic, J.N.3    Hwa, T.4    Szurmant, H.5
  • 30
    • 84872521100 scopus 로고    scopus 로고
    • Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models
    • Ekeberg M, Lovkvist C, Lan YH, Weigt M, Aurell E, (2013) Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models. Phys Rev E 87:
    • (2013) Phys Rev E , vol.87
    • Ekeberg, M.1    Lovkvist, C.2    Lan, Y.H.3    Weigt, M.4    Aurell, E.5
  • 31
    • 84886578448 scopus 로고    scopus 로고
    • The network of stabilizing contacts in proteins studied by coevolutionary data
    • Lui S, Tiana G, (2013) The network of stabilizing contacts in proteins studied by coevolutionary data. J Chem Phys 139:
    • (2013) J Chem Phys , vol.139
    • Lui, S.1    Tiana, G.2
  • 32
    • 84906706579 scopus 로고    scopus 로고
    • Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection
    • Morcos F, Schafer NP, Cheng RR, Onuchic JN, Wolynes PG, (2014) Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection. Proc Natl Acad Sci USA 111: 12408-12413.
    • (2014) Proc Natl Acad Sci USA , vol.111 , pp. 12408-12413
    • Morcos, F.1    Schafer, N.P.2    Cheng, R.R.3    Onuchic, J.N.4    Wolynes, P.G.5
  • 33
    • 84959188528 scopus 로고    scopus 로고
    • A many-body term improves the accuracy of effective potentials based on protein coevolutionary data
    • Contini A, Tiana G, (2015) A many-body term improves the accuracy of effective potentials based on protein coevolutionary data. J Chem Phys 143: 025103
    • (2015) J Chem Phys , vol.143 , pp. 025103
    • Contini, A.1    Tiana, G.2
  • 34
    • 3042677501 scopus 로고    scopus 로고
    • The effects of nonnative interactions on protein folding rates: Theory and simulation
    • Clementi C, Plotkin SS, (2004) The effects of nonnative interactions on protein folding rates: Theory and simulation. Protein Sci 13: 1750-1766.
    • (2004) Protein Sci , vol.13 , pp. 1750-1766
    • Clementi, C.1    Plotkin, S.S.2
  • 36
    • 84949981175 scopus 로고    scopus 로고
    • Evolution, energy landscapes and the paradoxes of protein folding
    • Wolynes PG, (2014) Evolution, energy landscapes and the paradoxes of protein folding. Biochimie http://dx.doi.org/ 10.1016/j.biochi.2014.12.007.
    • (2014) Biochimie
    • Wolynes, P.G.1
  • 37
    • 84890816704 scopus 로고    scopus 로고
    • Coevolutionary signals across protein lineages help capture multiple protein conformations
    • Morcos F, Jana B, Hwa T, Onuchic JN, (2013) Coevolutionary signals across protein lineages help capture multiple protein conformations. Proc Natl Acad Sci USA 110: 20533-20538.
    • (2013) Proc Natl Acad Sci USA , vol.110 , pp. 20533-20538
    • Morcos, F.1    Jana, B.2    Hwa, T.3    Onuchic, J.N.4
  • 38
    • 84896331026 scopus 로고    scopus 로고
    • From structure to function: The convergence of structure based models and co-evolutionary information
    • Jana B, Morcos F, Onuchic JN, (2014) From structure to function: The convergence of structure based models and co-evolutionary information. Phys Chem Chem Phys 16: 6496-6507.
    • (2014) Phys Chem Chem Phys , vol.16 , pp. 6496-6507
    • Jana, B.1    Morcos, F.2    Onuchic, J.N.3
  • 39
    • 58849083668 scopus 로고    scopus 로고
    • Quantitative criteria for native energetic heterogeneity influences in the prediction of protein folding kinetics
    • Cho SS, Levy Y, Wolynes PG, (2009) Quantitative criteria for native energetic heterogeneity influences in the prediction of protein folding kinetics. Proc Natl Acad Sci USA 106: 434-439.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 434-439
    • Cho, S.S.1    Levy, Y.2    Wolynes, P.G.3
  • 40
    • 55549098922 scopus 로고    scopus 로고
    • Changes of protein folding pathways by circular permutation - overlapping nuclei promote global cooperativity
    • Haglund E, Lindberg MO, Oliveberg M, (2008) Changes of protein folding pathways by circular permutation-overlapping nuclei promote global cooperativity. J Biol Chem 283: 27904-27915.
    • (2008) J Biol Chem , vol.283 , pp. 27904-27915
    • Haglund, E.1    Lindberg, M.O.2    Oliveberg, M.3
  • 41
    • 0036829967 scopus 로고    scopus 로고
    • Complete change of the protein folding transition state upon circular permutation
    • Lindberg M, Tangrot J, Oliveberg M, (2002) Complete change of the protein folding transition state upon circular permutation. Nature Struct Biol 9: 818-822.
    • (2002) Nature Struct Biol , vol.9 , pp. 818-822
    • Lindberg, M.1    Tangrot, J.2    Oliveberg, M.3
  • 42
    • 0032750509 scopus 로고    scopus 로고
    • The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved
    • Martinez JC, Serrano L, (1999) The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved. Nature Struct Biol 6: 1010-1016.
    • (1999) Nature Struct Biol , vol.6 , pp. 1010-1016
    • Martinez, J.C.1    Serrano, L.2
  • 43
    • 0026511656 scopus 로고
    • The folding of an enzyme. 1. Theory of protein engineering analysis of stability and pathway of protein folding
    • Fersht AR, Matouschek A, Serrano L, (1992) The folding of an enzyme. 1. Theory of protein engineering analysis of stability and pathway of protein folding. J Mol Biol 224: 771-782.
    • (1992) J Mol Biol , vol.224 , pp. 771-782
    • Fersht, A.R.1    Matouschek, A.2    Serrano, L.3
  • 44
    • 0024358426 scopus 로고
    • Mapping the transition-state and pathway of protein folding by protein engineering
    • Matouschek A, Kellis JT, Serrano L, Fersht AR, (1989) Mapping the transition-state and pathway of protein folding by protein engineering. Nature 340: 122-126.
    • (1989) Nature , vol.340 , pp. 122-126
    • Matouschek, A.1    Kellis, J.T.2    Serrano, L.3    Fersht, A.R.4
  • 45
    • 0037155413 scopus 로고    scopus 로고
    • Structural and energetic heterogeneity in protein folding. I. Theory
    • Plotkin SS, Onuchic JN, (2002) Structural and energetic heterogeneity in protein folding. I. Theory. J Chem Phys 116: 5263-5283.
    • (2002) J Chem Phys , vol.116 , pp. 5263-5283
    • Plotkin, S.S.1    Onuchic, J.N.2
  • 46
    • 2942705984 scopus 로고    scopus 로고
    • Gatekeepers in the ribosomal protein S6: Thermodynamics, kinetics, and folding pathways revealed by a minimalist protein model
    • Stoycheva AD, Brooks CL, Onuchic JN, (2004) Gatekeepers in the ribosomal protein S6: Thermodynamics, kinetics, and folding pathways revealed by a minimalist protein model. J Mol Biol 340: 571-585.
    • (2004) J Mol Biol , vol.340 , pp. 571-585
    • Stoycheva, A.D.1    Brooks, C.L.2    Onuchic, J.N.3
  • 47
    • 0037154268 scopus 로고    scopus 로고
    • Protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after the structural collapse
    • Cheung MS, Garcia AE, Onuchic JN, (2002) Protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after the structural collapse. Proc Natl Acad Sci U S A 99: 685-690.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 685-690
    • Cheung, M.S.1    Garcia, A.E.2    Onuchic, J.N.3
  • 48
    • 77649264931 scopus 로고    scopus 로고
    • Competition between native topology and nonnative interactions in simple and complex folding kinetics of natural and designed proteins
    • Zhang ZQ, Chan HS, (2010) Competition between native topology and nonnative interactions in simple and complex folding kinetics of natural and designed proteins. Proc Natl Acad Sci USA 107: 2920-2925.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 2920-2925
    • Zhang, Z.Q.1    Chan, H.S.2
  • 49
    • 0035826032 scopus 로고    scopus 로고
    • Role of explicitly cooperative interactions in protein folding funnels: A simulation study
    • Eastwood MP, Wolynes PG, (2001) Role of explicitly cooperative interactions in protein folding funnels: A simulation study. J Chem Phys 114: 4702-4716.
    • (2001) J Chem Phys , vol.114 , pp. 4702-4716
    • Eastwood, M.P.1    Wolynes, P.G.2
  • 54
    • 0031025991 scopus 로고    scopus 로고
    • Three-dimensional structure of the tyrosine kinase c-Src
    • Xu WQ, Harrison SC, Eck MJ, (1997) Three-dimensional structure of the tyrosine kinase c-Src. Nature 385: 595-602.
    • (1997) Nature , vol.385 , pp. 595-602
    • Xu, W.Q.1    Harrison, S.C.2    Eck, M.J.3
  • 55
    • 70449931860 scopus 로고    scopus 로고
    • Robustness and generalization of structure-based models for protein folding and function
    • Lammert H, Schug A, Onuchic JN, (2009) Robustness and generalization of structure-based models for protein folding and function. Proteins 77: 881-891.
    • (2009) Proteins , vol.77 , pp. 881-891
    • Lammert, H.1    Schug, A.2    Onuchic, J.N.3
  • 57
    • 84986519238 scopus 로고
    • The weighted gistogram analysis method for free-energy calculations on biomolecules.1. The method
    • Kumar S, Bouzida D, Swendsen RH, Kollman PA, Rosenberg JM, (1992) The weighted gistogram analysis method for free-energy calculations on biomolecules.1. The method. J Comput Chem 13: 1011-1021.
    • (1992) J Comput Chem , vol.13 , pp. 1011-1021
    • Kumar, S.1    Bouzida, D.2    Swendsen, R.H.3    Kollman, P.A.4    Rosenberg, J.M.5
  • 58
    • 36849122972 scopus 로고
    • High-temperature equation of state by a perturbation method.1. Nonpolar gases
    • Zwanzig RW, (1954) High-temperature equation of state by a perturbation method.1. Nonpolar gases. J Chem Phys 22: 1420-1426.
    • (1954) J Chem Phys , vol.22 , pp. 1420-1426
    • Zwanzig, R.W.1
  • 59
    • 0036293485 scopus 로고    scopus 로고
    • Conformational plasticity in folding of the split beta-alpha-beta protein S6: Evidence for burst-phase disruption of the native state
    • Otzen DE, Oliveberg M, (2002) Conformational plasticity in folding of the split beta-alpha-beta protein S6: Evidence for burst-phase disruption of the native state. J Mol Biol 317: 613-627.
    • (2002) J Mol Biol , vol.317 , pp. 613-627
    • Otzen, D.E.1    Oliveberg, M.2
  • 61
    • 2942590388 scopus 로고    scopus 로고
    • Simulation, experiment, and evolution: Understanding nucleation in protein S6 folding
    • Hubner IA, Oliveberg M, Shakhnovich EI, (2004) Simulation, experiment, and evolution: Understanding nucleation in protein S6 folding. Proc Natl Acad Sci USA 101: 8354-8359.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 8354-8359
    • Hubner, I.A.1    Oliveberg, M.2    Shakhnovich, E.I.3
  • 62
    • 84950149712 scopus 로고    scopus 로고
    • Constructing a folding model for protein S6 guided by dynamics deduced from NMR structures
    • submitted
    • Lammert H, Noel JK, Haglund E, Schug A, Onuchic JN, (2015) Constructing a folding model for protein S6 guided by dynamics deduced from NMR structures. J Chem Phys, submitted.
    • (2015) J Chem Phys
    • Lammert, H.1    Noel, J.K.2    Haglund, E.3    Schug, A.4    Onuchic, J.N.5
  • 63
    • 4444358276 scopus 로고    scopus 로고
    • Transition states for folding of circular-permuted proteins
    • Chen J, Wang J, Wang W, (2004) Transition states for folding of circular-permuted proteins. Proteins 57: 153-171.
    • (2004) Proteins , vol.57 , pp. 153-171
    • Chen, J.1    Wang, J.2    Wang, W.3
  • 67
    • 84870659790 scopus 로고    scopus 로고
    • The dominant folding route minimizes backbone distortion in SH3
    • Lammert H, Noel JK, Onuchic JN, (2012) The dominant folding route minimizes backbone distortion in SH3. Plos Comput Biol 8: E1002776
    • (2012) Plos Comput Biol , vol.8 , pp. e1002776
    • Lammert, H.1    Noel, J.K.2    Onuchic, J.N.3
  • 68
    • 84908154345 scopus 로고    scopus 로고
    • Biophysics of protein evolution and evolutionary protein biophysics
    • Sikosek T, Chan HS, (2014) Biophysics of protein evolution and evolutionary protein biophysics. J Royal Soc Interface 11: 20140419
    • (2014) J Royal Soc Interface , vol.11 , pp. 20140419
    • Sikosek, T.1    Chan, H.S.2
  • 69
    • 84946069451 scopus 로고    scopus 로고
    • UniProt: A hub for protein information
    • UniProt C, (2015) UniProt: A hub for protein information. Nucleic Acids Res 43: D204-D212.
    • (2015) Nucleic Acids Res , vol.43 , pp. D204-D212
    • UniProt, C.1
  • 70
    • 84930608409 scopus 로고    scopus 로고
    • Native contact density and nonnative hydrophobic effects in the folding of bacterial immunity proteins
    • Chen T, Chan HS, (2015) Native contact density and nonnative hydrophobic effects in the folding of bacterial immunity proteins. PLoS Comput Biol 11: E1004260
    • (2015) PLoS Comput Biol , vol.11 , pp. e1004260
    • Chen, T.1    Chan, H.S.2
  • 71
    • 0029919190 scopus 로고    scopus 로고
    • Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
    • Miyazawa S, Jernigan RL, (1996) Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol 256: 623-644.
    • (1996) J Mol Biol , vol.256 , pp. 623-644
    • Miyazawa, S.1    Jernigan, R.L.2
  • 72
    • 84927138881 scopus 로고    scopus 로고
    • Inverse Ising inference with correlated samples
    • Obermayer B, Levine E, (2014) Inverse Ising inference with correlated samples. New J Phys 16: 123017
    • (2014) New J Phys , vol.16 , pp. 123017
    • Obermayer, B.1    Levine, E.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.