메뉴 건너뛰기




Volumn , Issue , 2010, Pages 431-452

Conformational Search for the Protein Native State

Author keywords

Conformational search for protein native state Anfinsen experiments, to understand how amino acid sequence determines biologically active conformation; Enhanced sampling of conformational space; Protein "sample" its native state implementing MD approach systematically searching conformational space by numerically solving Newton's equations of motion

Indexed keywords


EID: 84888711909     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780470882207.ch19     Document Type: Chapter
Times cited : (20)

References (89)
  • 1
    • 0001189175 scopus 로고
    • Studies on denaturation of proteins XIII A theory of denaturation
    • H. Wu. Studies on denaturation of proteins XIII. A theory of denaturation. Chin J Physiol, 5 (4): 321-344, 1931.
    • (1931) Chin J Physiol , vol.5 , Issue.4 , pp. 321-344
    • Wu, H.1
  • 2
    • 0000648204 scopus 로고
    • On the structure of native, denatured and coagulated proteins
    • A.E. Mirsky and L. Pauling. On the structure of native, denatured and coagulated proteins. Proc Natl Acad Sci U S A, 22: 439-447, 1936.
    • (1936) Proc Natl Acad Sci U S A , vol.22 , pp. 439-447
    • Mirsky, A.E.1    Pauling, L.2
  • 3
    • 67349189383 scopus 로고
    • The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain
    • C.B. Anfinsen, E. Haber, M. Sela, and F.H. Jr. White. The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain. Proc Natl Acad Sci U S A, 47 (9): 1309-1314, 1961.
    • (1961) Proc Natl Acad Sci U S A , vol.47 , Issue.9 , pp. 1309-1314
    • Anfinsen, C.B.1    Haber, E.2    Sela, M.3    White Jr., F.H.4
  • 4
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • C.B. Anfinsen. Principles that govern the folding of protein chains. Science, 181 (4096): 223-230, 1973.
    • (1973) Science , vol.181 , Issue.4096 , pp. 223-230
    • Anfinsen, C.B.1
  • 6
    • 44949145113 scopus 로고    scopus 로고
    • Progress and challenges in protein structure prediction
    • Y. Zhang. Progress and challenges in protein structure prediction. Curr Opin Struct Biol, 18 (3): 342-348, 2008.
    • (2008) Curr Opin Struct Biol , vol.18 , Issue.3 , pp. 342-348
    • Zhang, Y.1
  • 7
    • 0345306764 scopus 로고    scopus 로고
    • Design of a novel globular protein fold with atomic-level accuracy
    • B. Kuhlman, G. Dantas, G.C. Ireton, G. Varani, B.L. Stoddard, and D. Baker. Design of a novel globular protein fold with atomic-level accuracy. Science, 302 (5649): 1364-1368, 2003.
    • (2003) Science , vol.302 , Issue.5649 , pp. 1364-1368
    • Kuhlman, B.1    Dantas, G.2    Ireton, G.C.3    Varani, G.4    Stoddard, B.L.5    Baker, D.6
  • 8
    • 0142116211 scopus 로고    scopus 로고
    • A reversible fragment assembly method for de novo protein structure prediction
    • G. Chikenji, Y. Fujitsuka, and S. Takada. A reversible fragment assembly method for de novo protein structure prediction. J Chem Phys, 119 (13): 6895-6903, 2003.
    • (2003) J Chem Phys , vol.119 , Issue.13 , pp. 6895-6903
    • Chikenji, G.1    Fujitsuka, Y.2    Takada, S.3
  • 9
    • 24944493938 scopus 로고    scopus 로고
    • Toward high-resolution de novo structure prediction for small proteins
    • P. Bradley, K.M.S. Misura, and D. Baker. Toward high-resolution de novo structure prediction for small proteins. Science, 309 (5742): 1868-1871, 2005.
    • (2005) Science , vol.309 , Issue.5742 , pp. 1868-1871
    • Bradley, P.1    Misura, K.M.S.2    Baker, D.3
  • 10
    • 33749572252 scopus 로고    scopus 로고
    • Minimalist representations and the importance of nearest neighbor effects in protein folding simulations
    • A. Colubri, A.K. Jha, M.-Y. Sheri, A. Sali, R.S. Berry, T.R. Sosnick, and K.F. Freed. Minimalist representations and the importance of nearest neighbor effects in protein folding simulations. J Mol Biol, 363 (4): 835-857, 2006.
    • (2006) J Mol Biol , vol.363 , Issue.4 , pp. 835-857
    • Colubri, A.1    Jha, A.K.2    Sheri, M.-Y.3    Sali, A.4    Berry, R.S.5    Sosnick, T.R.6    Freed, K.F.7
  • 12
    • 28044472257 scopus 로고    scopus 로고
    • Building native protein conformations from highly approximate backbone torsion angles
    • H. Gong, P.J. Fleming, and G.D. Rose. Building native protein conformations from highly approximate backbone torsion angles. Proc Natl Acad Sci U S A, 102 (45): 16227-16232, 2005.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , Issue.45 , pp. 16227-16232
    • Gong, H.1    Fleming, P.J.2    Rose, G.D.3
  • 14
    • 36749061828 scopus 로고    scopus 로고
    • Template-based modeling and free modeling by I-TASSER in CASP7
    • Y. Zhang. Template-based modeling and free modeling by I-TASSER in CASP7. Proteins, 8 (S1): 108-117, 2007.
    • (2007) Proteins , vol.8 , Issue.S1 , pp. 108-117
    • Zhang, Y.1
  • 15
    • 36749042541 scopus 로고    scopus 로고
    • Critical assessment of methods of protein structure prediction (GASP) round VII
    • J. Moult, K. Fidelis, A. Kryshtafovych, B. Rost, T. Hubbard, and A. Tramontano. Critical assessment of methods of protein structure prediction (GASP) round VII. Proteins, 69 (S8): 3-9, 2007.
    • (2007) Proteins , vol.69 , Issue.S8 , pp. 3-9
    • Moult, J.1    Fidelis, K.2    Kryshtafovych, A.3    Rost, B.4    Hubbard, T.5    Tramontano, A.6
  • 16
    • 0004146634 scopus 로고
    • Cambridge UK: Cambridge University Press
    • E. Schroedinger. What is Life? Cambridge, UK: Cambridge University Press, 1944.
    • (1944) What is Life?
    • Schroedinger, E.1
  • 18
    • 0034760077 scopus 로고    scopus 로고
    • Dynamic activation of protein function: A view emerging from NMR spetroscopy
    • A.J. Wand. Dynamic activation of protein function: A view emerging from NMR spetroscopy. Nat Struct Biol, 8 (11): 926-931, 2001.
    • (2001) Nat Struct Biol , vol.8 , Issue.11 , pp. 926-931
    • Wand, A.J.1
  • 19
    • 4243155782 scopus 로고    scopus 로고
    • NMR characterization of the dynamics of biomacromolecules
    • G.A. III Palmer. NMR characterization of the dynamics of biomacromolecules. Annu Rev Biophys Biomol Struct, 104 (8): 3623-3640, 2004.
    • (2004) Annu Rev Biophys Biomol Struct , vol.104 , Issue.8 , pp. 3623-3640
    • Palmer III, G.A.1
  • 21
    • 27744480205 scopus 로고    scopus 로고
    • Structural biology: Proteins fl ex to function
    • Y.P.J. Huang and G.T. Montellione. Structural biology: Proteins fl ex to function. Nature, 438 (7064): 36-37, 2005.
    • (2005) Nature , vol.438 , Issue.7064 , pp. 36-37
    • Huang, Y.P.J.1    Montellione, G.T.2
  • 22
    • 18744371588 scopus 로고    scopus 로고
    • Molecular dynamics and protein function
    • M. Karplus and J. Kuriyan. Molecular dynamics and protein function. Proc Natl Acad Sci U S A, 102 (19): 6679-6685, 2005.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , Issue.19 , pp. 6679-6685
    • Karplus, M.1    Kuriyan, J.2
  • 23
    • 33646922285 scopus 로고    scopus 로고
    • A statistical thermodynamic model of the protein ensemble
    • V.J. Hilser, B. Garcia-Moreno, G.T. Oas, G. Kapp, and S.T. Whitten. A statistical thermodynamic model of the protein ensemble. Chem Rev, 106 (5): 1545-1558, 2006.
    • (2006) Chem Rev , vol.106 , Issue.5 , pp. 1545-1558
    • Hilser, V.J.1    Garcia-Moreno, B.2    Oas, G.T.3    Kapp, G.4    Whitten, S.T.5
  • 24
    • 0028149160 scopus 로고
    • Exploring conformational space with a simple lattice model for protein structure
    • D.A. Hinds and M. Levitt. Exploring conformational space with a simple lattice model for protein structure. J Mol Biol, 243 (4): 668-682, 1994.
    • (1994) J Mol Biol , vol.243 , Issue.4 , pp. 668-682
    • Hinds, D.A.1    Levitt, M.2
  • 25
    • 0028203492 scopus 로고
    • Monte Carlo simulations of protein folding I. Lattice model and interaction scheme
    • A. Kolinski and J. Skolnick. Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme. Proteins, 18 (4): 338-352, 1994.
    • (1994) Proteins , vol.18 , Issue.4 , pp. 338-352
    • Kolinski, A.1    Skolnick, J.2
  • 26
    • 0032917636 scopus 로고    scopus 로고
    • Predicting the structures of 18 peptides using Geocore
    • K. Ishikawa, K. Yue, and K.A. Dill. Predicting the structures of 18 peptides using Geocore. Protein Sci, 8 (4): 716-721, 1999.
    • (1999) Protein Sci , vol.8 , Issue.4 , pp. 716-721
    • Ishikawa, K.1    Yue, K.2    Dill, K.A.3
  • 27
    • 0029063717 scopus 로고
    • The complexity and accuracy of discrete state models of protein structure
    • B.H. Park and M. Levitt. The complexity and accuracy of discrete state models of protein structure. J Mol Biol, 249 (2): 493-507, 1995.
    • (1995) J Mol Biol , vol.249 , Issue.2 , pp. 493-507
    • Park, B.H.1    Levitt, M.2
  • 28
    • 0030017791 scopus 로고    scopus 로고
    • Adjusting potential energy functions for lattice models of chain molecules
    • B.A. Reva, A.V. Finkelstein, M.F. Sanner, and A.J. Olson. Adjusting potential energy functions for lattice models of chain molecules. Proteins, 25 (3): 379-388, 1996.
    • (1996) Proteins , vol.25 , Issue.3 , pp. 379-388
    • Reva, B.A.1    Finkelstein, A.V.2    Sanner, M.F.3    Olson, A.J.4
  • 29
    • 0002006297 scopus 로고
    • Are there pathways for protein folding?
    • C. Levinthal. Are there pathways for protein folding? J Chem Phys, 65 (1): 44-45, 1968.
    • (1968) J Chem Phys , vol.65 , Issue.1 , pp. 44-45
    • Levinthal, C.1
  • 30
    • 0024750637 scopus 로고
    • A lattice statistical mechanics model of the conformational and sequence spaces of proteins
    • K.F. Lau and A.K. Dill. A lattice statistical mechanics model of the conformational and sequence spaces of proteins. Macromolecules, 22 (10): 3986-3997, 1989.
    • (1989) Macromolecules , vol.22 , Issue.10 , pp. 3986-3997
    • Lau, K.F.1    Dill, A.K.2
  • 31
    • 0027690211 scopus 로고
    • Finding lowest free energy conformation of a protein is an NP-hard problem: Proof and implications
    • R. Unger and J. Moult. Finding lowest free energy conformation of a protein is an NP-hard problem: Proof and implications. Bull Math Biol, 55 (6): 1183-1198, 1993.
    • (1993) Bull Math Biol , vol.55 , Issue.6 , pp. 1183-1198
    • Unger, R.1    Moult, J.2
  • 32
    • 0030901866 scopus 로고    scopus 로고
    • Robust proofs of NP-hardness for protein folding: General lattices and energy potentials
    • W.E. Hart and S. Istrail. Robust proofs of NP-hardness for protein folding: General lattices and energy potentials. J Comp Biol, 4 (1): 1-22, 1997.
    • (1997) J Comp Biol , vol.4 , Issue.1 , pp. 1-22
    • Hart, W.E.1    Istrail, S.2
  • 33
    • 0031465967 scopus 로고    scopus 로고
    • New view of protein folding reconciled with the old through multiple unfolding simulations
    • T. Lazaridis and M. Karplus. New view of protein folding reconciled with the old through multiple unfolding simulations. Science, 278 (5345): 1928-1931, 1997.
    • (1997) Science , vol.278 , Issue.5345 , pp. 1928-1931
    • Lazaridis, T.1    Karplus, M.2
  • 34
    • 1842298212 scopus 로고    scopus 로고
    • From Levinthal to pathways to funnels
    • K.A. Dill and H.S. Chan. From Levinthal to pathways to funnels. Nat Struct Biol, 4 (1): 10-19, 1997.
    • (1997) Nat Struct Biol , vol.4 , Issue.1 , pp. 10-19
    • Dill, K.A.1    Chan, H.S.2
  • 35
    • 0030628825 scopus 로고    scopus 로고
    • Theory of protein folding: The energy landscape perspective
    • J.N. Onuchic, Z. Luthey-Schulten, and P.G. Wolynes. Theory of protein folding: The energy landscape perspective. Annu Rev Phys Chem, 48: 545-600, 1997.
    • (1997) Annu Rev Phys Chem , vol.48 , pp. 545-600
    • Onuchic, J.N.1    Luthey-Schulten, Z.2    Wolynes, P.G.3
  • 36
    • 0000370391 scopus 로고    scopus 로고
    • The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics
    • O.M. Becker and M. Karplus. The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics. J Chem Phys, 106 (4): 1495-1517, 1997.
    • (1997) J Chem Phys , vol.106 , Issue.4 , pp. 1495-1517
    • Becker, O.M.1    Karplus, M.2
  • 37
    • 0036535895 scopus 로고    scopus 로고
    • Protein folding: The free energy surface
    • M. Gruebele. Protein folding: The free energy surface. Curr Opin Struct Biol, 12 (2): 161-168, 2002.
    • (2002) Curr Opin Struct Biol , vol.12 , Issue.2 , pp. 161-168
    • Gruebele, M.1
  • 38
    • 39149100599 scopus 로고    scopus 로고
    • Coarse-grained models of protein folding: Toy-models or predictive tools?
    • C. Clementi. Coarse-grained models of protein folding: Toy-models or predictive tools? Curr Opin Struct Biol, 18 (1): 10-15, 2008.
    • (2008) Curr Opin Struct Biol , vol.18 , Issue.1 , pp. 10-15
    • Clementi, C.1
  • 39
    • 15244355250 scopus 로고    scopus 로고
    • The relationship between the fl exibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking
    • G.R. Smith, M.J.E. Sternberg, and P.A. Bates. The relationship between the fl exibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking. J Mol Biol, 347 (5): 1077-1101, 2005.
    • (2005) J Mol Biol , vol.347 , Issue.5 , pp. 1077-1101
    • Smith, G.R.1    Sternberg, M.J.E.2    Bates, P.A.3
  • 40
    • 0032544060 scopus 로고    scopus 로고
    • The structural distribution of cooperative interactions in proteins: Analysis of the native state ensemble
    • V.J. Hilser, T. Oas, D. Dowdy, and E. Freire. The structural distribution of cooperative interactions in proteins: Analysis of the native state ensemble. Proc Natl Acad Sci U S A, 95 (17): 9903-9908, 1998.
    • (1998) Proc Natl Acad Sci U S A , vol.95 , Issue.17 , pp. 9903-9908
    • Hilser, V.J.1    Oas, T.2    Dowdy, D.3    Freire, E.4
  • 42
    • 68149125150 scopus 로고    scopus 로고
    • Multiscale characterization of protein conformational ensembles
    • A. Shehu, L.E. Kavraki, and C. Clementi. Multiscale characterization of protein conformational ensembles. Proteins, 76 (4): 837-851, 2009.
    • (2009) Proteins , vol.76 , Issue.4 , pp. 837-851
    • Shehu, A.1    Kavraki, L.E.2    Clementi, C.3
  • 43
    • 0028286471 scopus 로고
    • Kinetics versus thermodynamics in protein folding
    • D. Baker and D.A. Agard. Kinetics versus thermodynamics in protein folding. Biochemistry, 33 (24): 7505-7509, 1994.
    • (1994) Biochemistry , vol.33 , Issue.24 , pp. 7505-7509
    • Baker, D.1    Agard, D.A.2
  • 44
    • 0032510675 scopus 로고    scopus 로고
    • On the thermodynamic hypothesis of protein folding
    • S. Govindarajan and R.A. Goldstein. On the thermodynamic hypothesis of protein folding. Proc Natl Acad Sci U S A, 95 (10): 5545-5549, 1997.
    • (1997) Proc Natl Acad Sci U S A , vol.95 , Issue.10 , pp. 5545-5549
    • Govindarajan, S.1    Goldstein, R.A.2
  • 46
    • 33644760365 scopus 로고    scopus 로고
    • Shaping up the protein folding funnel by local interaction: lesson from a structure prediction study
    • G. Chikenji, Y. Fujitsuka, and S. Takada. Shaping up the protein folding funnel by local interaction: lesson from a structure prediction study. Proc Natl Acad Sci U S A, 103 (9): 3141-3146, 2006.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , Issue.9 , pp. 3141-3146
    • Chikenji, G.1    Fujitsuka, Y.2    Takada, S.3
  • 47
    • 33745611125 scopus 로고    scopus 로고
    • Low-dimensional free energy landscapes of protein folding reactions by nonlinear dimensionality reduction
    • P. Das, M. Moll, H. Stamati, L.E. Kavraki, and C. Clementi. Low-dimensional free energy landscapes of protein folding reactions by nonlinear dimensionality reduction . Proc Natl Acad Sci U S A, 103 (26): 9885-9890, 2006.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , Issue.26 , pp. 9885-9890
    • Das, P.1    Moll, M.2    Stamati, H.3    Kavraki, L.E.4    Clementi, C.5
  • 48
    • 0023430366 scopus 로고
    • Monte Carlo-minimization approach to the multiple -minima problem in protein folding
    • Z. Li and H.A. Scheraga. Monte Carlo-minimization approach to the multiple -minima problem in protein folding. Proc Natl Acad Sci U S A, 84 (19): 6611-6615, 1987.
    • (1987) Proc Natl Acad Sci U S A , vol.84 , Issue.19 , pp. 6611-6615
    • Li, Z.1    Scheraga, H.A.2
  • 49
    • 0027955787 scopus 로고
    • Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins
    • R. Abagyan and M. Totrov. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J Mol Biol, 235 (3): 983-1002, 1994.
    • (1994) J Mol Biol , vol.235 , Issue.3 , pp. 983-1002
    • Abagyan, R.1    Totrov, M.2
  • 50
    • 3042846748 scopus 로고    scopus 로고
    • Determination of ensembles of structures consistent with NMR order parameters
    • R.B. Best and M. Vendruscolo. Determination of ensembles of structures consistent with NMR order parameters. J Am Chem Soc, 126 (26): 8090-8091, 2004.
    • (2004) J Am Chem Soc , vol.126 , Issue.26 , pp. 8090-8091
    • Best, R.B.1    Vendruscolo, M.2
  • 51
    • 33748281380 scopus 로고    scopus 로고
    • Modeling protein conformational ensembles: From missing loops to equilibrium fl uctuations
    • A. Shehu, C. Clementi, and L.E. Kavraki. Modeling protein conformational ensembles: From missing loops to equilibrium fl uctuations. Proteins, 65 (1): 164 - 179, 2006.
    • (2006) Proteins , vol.65 , Issue.1 , pp. 164-179
    • Shehu, A.1    Clementi, C.2    Kavraki, L.E.3
  • 52
    • 0016696599 scopus 로고
    • Studies on protein folding, unfolding and fl uctuations by computer simulation: The effect of specific amino acid sequence represented by specific inter-unit interactions
    • H. Taketomi, Y. Ueda, and N. Go. Studies on protein folding, unfolding and fl uctuations by computer simulation: The effect of specific amino acid sequence represented by specific inter-unit interactions. Int J Pept Protein Res, 7 (6): 445-459, 1975.
    • (1975) Int J Pept Protein Res , vol.7 , Issue.6 , pp. 445-459
    • Taketomi, H.1    Ueda, Y.2    Go, N.3
  • 54
    • 2542617639 scopus 로고    scopus 로고
    • Geometry and symmetry presculpt the free-energy landscape of proteins
    • T.H. Hoang, A. Trovato, F. Seno, J.R. Banavar, and A. Maritan. Geometry and symmetry presculpt the free-energy landscape of proteins. Proc Natl Acad Sci U S A, 101 (21): 7960-7964, 2007.
    • (2007) Proc Natl Acad Sci U S A , vol.101 , Issue.21 , pp. 7960-7964
    • Hoang, T.H.1    Trovato, A.2    Seno, F.3    Banavar, J.R.4    Maritan, A.5
  • 56
    • 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?
    • S. Matysiak and C. Clementi. 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 (8): 235-248, 2004.
    • (2004) J Mol Biol , vol.343 , Issue.8 , pp. 235-248
    • Matysiak, S.1    Clementi, C.2
  • 57
    • 22544446147 scopus 로고    scopus 로고
    • Balancing energy and entropy: A minimalist model for the characterization of protein folding landscapes
    • P. Das, S. Matysiak, and C. Clementi. Balancing energy and entropy: A minimalist model for the characterization of protein folding landscapes. Proc Natl Acad Sci U S A, 102 (29): 10141-10146, 2005.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , Issue.29 , pp. 10141-10146
    • Das, P.1    Matysiak, S.2    Clementi, C.3
  • 58
    • 33748770940 scopus 로고    scopus 로고
    • Minimalist protein model as a diagnostic tool for misfolding and aggregation
    • S. Matysiak and C. Clementi. Minimalist protein model as a diagnostic tool for misfolding and aggregation. J Mol Biol, 363 (1): 297-308, 2006.
    • (2006) J Mol Biol , vol.363 , Issue.1 , pp. 297-308
    • Matysiak, S.1    Clementi, C.2
  • 59
    • 0033557350 scopus 로고    scopus 로고
    • Backbone dynamics, fast folding, and secondary structure formation in helical proteins and peptides
    • C. Hardin, Z. Luthey-Schulten, and P.G. Wolynes. Backbone dynamics, fast folding, and secondary structure formation in helical proteins and peptides. Proteins, 34 (3): 281-294, 1999.
    • (1999) Proteins , vol.34 , Issue.3 , pp. 281-294
    • Hardin, C.1    Luthey-Schulten, Z.2    Wolynes, P.G.3
  • 60
    • 27144440086 scopus 로고    scopus 로고
    • Efficient sampling of protein structures by model hopping
    • W. Kwak and U.H. Hansmann. Efficient sampling of protein structures by model hopping. Phys Rev Lett, 95 (13): 138102, 2005.
    • (2005) Phys Rev Lett , vol.95 , Issue.13
    • Kwak, W.1    Hansmann, U.H.2
  • 62
    • 34547926023 scopus 로고    scopus 로고
    • Multigraining: An algorithm for simultaneous fine-grained and coarse-grained simulation of molecular systems
    • S. Christakos, C. Gabrielides, and W.B. Rhoten. Multigraining: An algorithm for simultaneous fine-grained and coarse-grained simulation of molecular systems. J Chem Phys, 125 (15): 154106, 2006.
    • (2006) J Chem Phys , vol.125 , Issue.15
    • Christakos, S.1    Gabrielides, C.2    Rhoten, W.B.3
  • 63
    • 34447515841 scopus 로고    scopus 로고
    • From coarse-grain to all-atom: Towards multiscale analysis of protein landscapes
    • A.P. Heath, L.F. Kavraki, and C. Clementi. From coarse-grain to all-atom: Towards multiscale analysis of protein landscapes. Proteins, 68 (3): 646-661, 2007.
    • (2007) Proteins , vol.68 , Issue.3 , pp. 646-661
    • Heath, A.P.1    Kavraki, L.F.2    Clementi, C.3
  • 64
    • 39549115231 scopus 로고    scopus 로고
    • Unfolding the fold of cyclic cysteine-rich peptides
    • A. Shehu, L.E. Kavraki, and C. Clementi. Unfolding the fold of cyclic cysteine-rich peptides. Protein Sci, 17 (3): 482-493, 2008.
    • (2008) Protein Sci , vol.17 , Issue.3 , pp. 482-493
    • Shehu, A.1    Kavraki, L.E.2    Clementi, C.3
  • 66
    • 0032561237 scopus 로고    scopus 로고
    • Pathways to a protein folding intermediate observed in a 1-μ s simulation in aqueous solution
    • Y. Duan and Y.A. Kollman. Pathways to a protein folding intermediate observed in a 1-μ s simulation in aqueous solution. Science, 282 (5389): 740-744, 1998.
    • (1998) Science , vol.282 , Issue.5389 , pp. 740-744
    • Duan, Y.1    Kollman, Y.A.2
  • 67
    • 0034623787 scopus 로고    scopus 로고
    • Computing: Screen savers of the world unite!
    • M. Shirts and V.J. Pande. Computing: Screen savers of the world unite! Science, 290 (5498): 1903-1904, 2000.
    • (2000) Science , vol.290 , Issue.5498 , pp. 1903-1904
    • Shirts, M.1    Pande, V.J.2
  • 68
    • 0037934616 scopus 로고    scopus 로고
    • Understanding folding and design: Replica-exchange simulations of Trp-cage miniproteins
    • J.W. Pitera and W. Swope. Understanding folding and design: Replica-exchange simulations of Trp-cage miniproteins. Proc Natl Acad Sci U S A, 100 (13): 7587 - 7592, 2003.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , Issue.13 , pp. 7587-7592
    • Pitera, J.W.1    Swope, W.2
  • 69
    • 46249090563 scopus 로고    scopus 로고
    • Anton, a special-purpose machine for molecular dynamics simulation
    • D.E. Shaw et al. Anton, a special-purpose machine for molecular dynamics simulation . Commun ACM, 51 (7): 91-97, 2008.
    • (2008) Commun ACM , vol.51 , Issue.7 , pp. 91-97
    • Shaw, D.E.1
  • 70
    • 2542462060 scopus 로고    scopus 로고
    • Folding of the villin headpiece subdomain from random structures Analysis of the charge distribution as a function of pH
    • D.R. Ripoll, J.A. Vila, and H.A. Scheraga. Folding of the villin headpiece subdomain from random structures. Analysis of the charge distribution as a function of pH. J Mol Biol, 339 (4): 915-925, 2004.
    • (2004) J Mol Biol , vol.339 , Issue.4 , pp. 915-925
    • Ripoll, D.R.1    Vila, J.A.2    Scheraga, H.A.3
  • 72
    • 1542317796 scopus 로고    scopus 로고
    • How much backbone motion in ubiquitin is required to account for dipolar coupling data measured in multiple alignment media as assessed by independent cross-validation?
    • G.M. Clore and C.D. Schwieters. How much backbone motion in ubiquitin is required to account for dipolar coupling data measured in multiple alignment media as assessed by independent cross-validation? J Am Chem Soc, 126 (9): 2923 - 2938, 2004.
    • (2004) J Am Chem Soc , vol.126 , Issue.9 , pp. 2923-2938
    • Clore, G.M.1    Schwieters, C.D.2
  • 73
    • 29444446536 scopus 로고    scopus 로고
    • Concordance of residual dipolar couplings, backbone order parameters and crystallographic B-factors for a small α / β protein: A unified picture of high probability, fast atomic motions in proteins
    • G.M. Clore and C.D. Schwieters. Concordance of residual dipolar couplings, backbone order parameters and crystallographic B-factors for a small α / β protein: A unified picture of high probability, fast atomic motions in proteins. J Mol Biol, 355 (5): 879-886, 2006.
    • (2006) J Mol Biol , vol.355 , Issue.5 , pp. 879-886
    • Clore, G.M.1    Schwieters, C.D.2
  • 74
    • 33846532929 scopus 로고    scopus 로고
    • The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins
    • B. Richter, J. Gsponer, P. Várnai, X. Salvatella, and M. Vendruscolo. The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins. J Biomol NMR, 37 (2): 117-135, 2007.
    • (2007) J Biomol NMR , vol.37 , Issue.2 , pp. 117-135
    • Richter, B.1    Gsponer, J.2    Várnai, P.3    Salvatella, X.4    Vendruscolo, M.5
  • 75
    • 33748518255 scopus 로고    scopus 로고
    • Comparison of multiple amber force fields and development of improved protein backbone parameters
    • V. Hornak, R. Abel, A. Okur, B. Strockbine, A. Roitberg, and C. Simmerling. Comparison of multiple amber force fields and development of improved protein backbone parameters. Proteins, 65 (3): 712-725, 2006.
    • (2006) Proteins , vol.65 , Issue.3 , pp. 712-725
    • Hornak, V.1    Abel, R.2    Okur, A.3    Strockbine, B.4    Roitberg, A.5    Simmerling, C.6
  • 76
    • 36448983552 scopus 로고    scopus 로고
    • Creating protein models from electron-density maps using particle -filtering methods
    • F. DiMao, D. Kondrashov, E. Bitto, A. Soni, G. Bingman, G. Phillips, and J. Shavlik. Creating protein models from electron-density maps using particle -filtering methods. Bioinformatics, 23 (21): 2851-2858, 2007.
    • (2007) Bioinformatics , vol.23 , Issue.21 , pp. 2851-2858
    • DiMao, F.1    Kondrashov, D.2    Bitto, E.3    Soni, A.4    Bingman, G.5    Phillips, G.6    Shavlik, J.7
  • 77
    • 33748271512 scopus 로고    scopus 로고
    • Structure determination of symmetric homo-oligomers by a complete search of symmetry configuration space, using NMR restraints and van der Waals packing
    • S. Potluri, A.K. Yarr, J.J. Chou, B.R. Donald, and C. Bailey-Kellogg. Structure determination of symmetric homo-oligomers by a complete search of symmetry configuration space, using NMR restraints and van der Waals packing. Proteins, 65 (1): 203-219, 2006.
    • (2006) Proteins , vol.65 , Issue.1 , pp. 203-219
    • Potluri, S.1    Yarr, A.K.2    Chou, J.J.3    Donald, B.R.4    Bailey-Kellogg, C.5
  • 78
    • 34547472077 scopus 로고    scopus 로고
    • Sampling conformation space to model equilibrium fl uctuations in proteins
    • A. Shehu, C. Clementi, and L.E. Kavraki. Sampling conformation space to model equilibrium fl uctuations in proteins. Algorithmica, 48 (4): 303-327, 2007.
    • (2007) Algorithmica , vol.48 , Issue.4 , pp. 303-327
    • Shehu, A.1    Clementi, C.2    Kavraki, L.E.3
  • 79
    • 27744471408 scopus 로고    scopus 로고
    • Constrained geometric simulation of diffusive motion in proteins
    • S. Wells, S. Menor, B. Hespenheide, and M.F. Thorpe. Constrained geometric simulation of diffusive motion in proteins. J Phys Biol, 2 (4): 127-136, 2005.
    • (2005) J Phys Biol , vol.2 , Issue.4 , pp. 127-136
    • Wells, S.1    Menor, S.2    Hespenheide, B.3    Thorpe, M.F.4
  • 81
    • 33847776838 scopus 로고    scopus 로고
    • On the characterization of protein native state ensembles
    • A. Shehu, L.E. Kavraki, and C. Clementi. On the characterization of protein native state ensembles. Biophys J, 92 (5): 1503-1511, 2007.
    • (2007) Biophys J , vol.92 , Issue.5 , pp. 1503-1511
    • Shehu, A.1    Kavraki, L.E.2    Clementi, C.3
  • 84
    • 34948869804 scopus 로고    scopus 로고
    • The ultimate speed limit to protein folding is conformational searching
    • K. Ghosh, S.B. Ozkan, and K.A. Dill. The ultimate speed limit to protein folding is conformational searching. J Am Chem Soc, 129 (39): 11920-11927, 2007.
    • (2007) J Am Chem Soc , vol.129 , Issue.39 , pp. 11920-11927
    • Ghosh, K.1    Ozkan, S.B.2    Dill, K.A.3
  • 86
    • 84888763200 scopus 로고    scopus 로고
    • An Ab-initio tree-based exploration to enhance sampling of low-energy protein conformations
    • J. Trinkle, Y. Matsuoka, and J.A. Castellanos (Eds.), Seattle, WA, June
    • A. Shehu. An Ab-initio tree-based exploration to enhance sampling of low-energy protein conformations. In Proceedings of Robotics: Science and Systems, J. Trinkle, Y. Matsuoka, and J.A. Castellanos (Eds.), pp. 31-39. Seattle, WA, June, 2009.
    • (2009) Proceedings of Robotics: Science and Systems , pp. 31-39
    • Shehu, A.1
  • 88
    • 0345701546 scopus 로고    scopus 로고
    • Hierarchical protein folding pathways: A computational study of protein fragments
    • N. Haspel, C.J. Tsai, H. Wolfson, and R. Nussinov. Hierarchical protein folding pathways: A computational study of protein fragments. Proteins, 51 (2): 203-215, 2003.
    • (2003) Proteins , vol.51 , Issue.2 , pp. 203-215
    • Haspel, N.1    Tsai, C.J.2    Wolfson, H.3    Nussinov, R.4
  • 89
    • 70349317510 scopus 로고    scopus 로고
    • Restriction vs. guidance: Fragment assembly and associative memory Hamiltonians for protein structure prediction
    • J. Hegler, J. Laetzer, A. Shehu, C. Clementi, and P.G. Wolynes. Restriction vs. guidance: Fragment assembly and associative memory Hamiltonians for protein structure prediction. Proc Natl Acad Sci U S A, 106 (36): 15302-15307, 2009.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , Issue.36 , pp. 15302-15307
    • Hegler, J.1    Laetzer, J.2    Shehu, A.3    Clementi, C.4    Wolynes, P.G.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.