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Volumn 9, Issue 3, 2011, Pages 383-398

In search of the protein native state with a probabilistic sampling approach

Author keywords

conformational ensemble; fragment library; probabilistic search; Protein native state; tree based projection guided exploration

Indexed keywords

PEPTIDE FRAGMENT; PEPTIDE LIBRARY; PROTEIN;

EID: 79959253922     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720011005574     Document Type: Article
Times cited : (25)

References (38)
  • 1
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • Anfinsen CB, 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
  • 2
    • 0026320866 scopus 로고
    • The energy landscapes and motion on proteins
    • Frauenfelder H, Sligar SG, Wolynes PG, The energy landscapes and motion on proteins, Science 254(5038):1598-1603, 1991.
    • (1991) Science , vol.254 , Issue.5038 , pp. 1598-1603
    • Frauenfelder, H.1    Sligar, S.G.2    Wolynes, P.G.3
  • 3
    • 1842298212 scopus 로고    scopus 로고
    • From levinthal to pathways to funnels
    • DOI 10.1038/nsb0197-10
    • Dill KA, Chan HS, From levinthal to pathways to funnels, Nat Struct Biol 4(1):10-19, 1997. (Pubitemid 27020916)
    • (1997) Nature Structural Biology , vol.4 , Issue.1 , pp. 10-19
    • Dill, K.A.1    Chan, H.S.2
  • 4
    • 27744480205 scopus 로고    scopus 로고
    • Structural biology: Proteins flex to function
    • Huang YPJ, Montellione GT, Structural biology: Proteins flex 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
  • 6
    • 24944493938 scopus 로고    scopus 로고
    • Biochemistry: Toward high-resolution de novo structure prediction for small proteins
    • DOI 10.1126/science.1113801
    • Bradley P, Misura KMS, Baker D, Toward high-resolution de novo structure prediction for small proteins, Science 309(5742):1868-1871, 2005. (Pubitemid 41325099)
    • (2005) Science , vol.309 , Issue.5742 , pp. 1868-1871
    • Bradley, P.1    Misura, K.M.S.2    Baker, D.3
  • 7
    • 34249777526 scopus 로고    scopus 로고
    • Eris: An automated estimator of protein stability [2]
    • DOI 10.1038/nmeth0607-466, PII NMETH0607-466
    • Yin S, Ding F, Dokholyan NV, Eris: An automated estimator of protein stability, Nat Methods 4(6):466-467, 2007. (Pubitemid 46852064)
    • (2007) Nature Methods , vol.4 , Issue.6 , pp. 466-467
    • Yin, S.1    Ding, F.2    Dokholyan, N.V.3
  • 8
    • 1042298843 scopus 로고    scopus 로고
    • Computational design of protein-protein interactions
    • DOI 10.1016/j.cbpa.2003.12.008
    • Kortemme T, Baker D, Computational design of protein-protein interactions, Curr Opinion Struct Biol 8(1):91-97, 2004. (Pubitemid 38201483)
    • (2004) Current Opinion in Chemical Biology , vol.8 , Issue.1 , pp. 91-97
    • Kortemme, T.1    Baker, D.2
  • 9
    • 0042511005 scopus 로고    scopus 로고
    • A graph-theory algorithm for rapid protein side-chain prediction
    • DOI 10.1110/ps.03154503
    • Canutescu AA, Shelenkov AA, Dunbrack Jr RL. A graph-theory algorithm for rapid protein side chain prediction, Protein Sci 12(9):2001-2014, 2003. (Pubitemid 37022822)
    • (2003) Protein Science , vol.12 , Issue.9 , pp. 2001-2014
    • Canutescu, A.A.1    Shelenkov, A.A.2    Dunbrack Jr., R.L.3
  • 10
    • 34447515841 scopus 로고    scopus 로고
    • From coarse-grain to all-atom: Toward multiscale analysis of protein landscapes
    • DOI 10.1002/prot.21371
    • Heath AP, Kavraki LE, Clementi C. From coarse-grain to all-atom: Towards multiscale analysis of protein landscapes, Proteins: Struct Funct Bioinf 68(3):646-661, 2007. (Pubitemid 47068305)
    • (2007) Proteins: Structure, Function and Genetics , vol.68 , Issue.3 , pp. 646-661
    • Heath, A.P.1    Kavraki, L.E.2    Clementi, C.3
  • 11
    • 39149100599 scopus 로고    scopus 로고
    • Coarse-grained models of protein folding: Toy-models or predictive tools
    • Clementi C, Coarse-grained models of protein folding: Toy-models or predictive tools? Curr Opin Struct Biol 18:10-15, 2008.
    • (2008) Curr. Opin. Struct. Biol. , vol.18 , pp. 10-15
    • Clementi, C.1
  • 12
    • 79959375397 scopus 로고    scopus 로고
    • An ab initio tree-based exploration to enhance sampling of low-energy protein conformations
    • Trinkle J Matsuoka Y Castellanos JA Seattle WA USA
    • Shehu A, An ab initio tree-based exploration to enhance sampling of low-energy protein conformations, in Trinkle J, Matsuoka Y, Castellanos JA, Robotics: Science and Systems V, pp. 241-248, Seattle, WA, USA, 2009.
    • (2009) Robotics: Science and Systems V. , pp. 241-248
    • Shehu, A.1
  • 13
    • 57249105450 scopus 로고    scopus 로고
    • Planning among movable obstacles with artificial constraints
    • Stilman M, Kuffner JJ, Planning among movable obstacles with artificial constraints, Int J Robot Res 12(12):1295-1307, 2008.
    • (2008) Int. J. Robot Res. , vol.12 , Issue.12 , pp. 1295-1307
    • Stilman, M.1    Kuffner, J.J.2
  • 14
    • 0036458038 scopus 로고    scopus 로고
    • On delaying collision checking in PRM planning: Application to multi-robot coordination
    • Sánchez G, Latombe JC, On delaying collision checking in PRM planning: Application to multi-robot coordination, Int J Robot Res 21(1):5-26, 2002.
    • (2002) Int. J. Robot. Res. , vol.21 , Issue.1 , pp. 5-26
    • Sánchez, G.1    Latombe, J.C.2
  • 15
    • 51649128820 scopus 로고    scopus 로고
    • Discrete search leading continuous exploration for kinodynamic motion planning
    • Atlanta GA USA
    • Plaku E, Kavraki L, Vardi M, Discrete search leading continuous exploration for kinodynamic motion planning, in Robotics: Science and Systems, Atlanta, GA, USA, 2007.
    • (2007) Robotics: Science and Systems
    • Plaku, E.1    Kavraki, L.2    Vardi, M.3
  • 16
    • 84959454477 scopus 로고    scopus 로고
    • Efficient motion planning based on disassembly
    • Cambridge MA
    • Yang Y, Brock O, Efficient motion planning based on disassembly, in Robotics: Science and Systems, pp. 97-104, Cambridge, MA, 2005.
    • (2005) Robotics: Science and Systems , pp. 97-104
    • Yang, Y.1    Brock, O.2
  • 17
    • 33747610281 scopus 로고    scopus 로고
    • Motion planning in the presence of drift, underactuation and discrete system changes
    • Boston MA
    • Ladd AM, Kavraki LE, Motion planning in the presence of drift, underactuation and discrete system changes, in Robotics: Science and Systems, pp. 233-241, Boston, MA, 2005.
    • (2005) Robotics: Science and Systems , pp. 233-241
    • Ladd, A.M.1    Kavraki, L.E.2
  • 18
    • 53849129958 scopus 로고    scopus 로고
    • Workspace-based connectivity oracle: An adaptive sampling strategy for PRM planning
    • Springer Tracts in Advanced Robotics New York NY
    • Kurniawati H, Hsu D, Workspace-based connectivity oracle: An adaptive sampling strategy for PRM planning, in WAFR, Volume 47 of Springer Tracts in Advanced Robotics, pp. 35-51, New York, NY, 2006.
    • (2006) WAFR , vol.47 , pp. 35-51
    • Kurniawati, H.1    Hsu, D.2
  • 19
    • 53849121997 scopus 로고    scopus 로고
    • RESAMPL: A region-sensitive adaptive motion planner
    • Springer Tracts in Advanced Robotics
    • Rodriguez S, Thomas S, Pearce R, Amato NM, RESAMPL: A region-sensitive adaptive motion planner, in WAFR, Volume 47 of Springer Tracts in Advanced Robotics, pp. 285-300, 2006.
    • (2006) WAFR , vol.47 , pp. 285-300
    • Rodriguez, S.1    Thomas, S.2    Pearce, R.3    Amato, N.M.4
  • 21
    • 29144459602 scopus 로고    scopus 로고
    • Using workspace information as a guide to non-uniform sampling in probabilistic roadmap planners
    • DOI 10.1177/0278364905060132
    • Jur P, van den Berg, Overmars MH, Using workspace information as a guide to nonuniform sampling in probabilistic roadmap planners, Int J Robot Res 24(12):1055-1071, 2005. (Pubitemid 41807373)
    • (2005) International Journal of Robotics Research , vol.24 , Issue.12 , pp. 1055-1071
    • Van Den Berg, J.P.1    Overmars, M.H.2
  • 22
    • 0001176785 scopus 로고    scopus 로고
    • New optimization method for conformational energy calculations on polypeptides: Conformational space annealing
    • Lee J, Scheraga HA, Rackovsky S, New optimization method for conformational energy calculations on polypeptides: Conformational space annealing, J Comput Chem 18(9):1222-1232, 1997. (Pubitemid 127650577)
    • (1997) Journal of Computational Chemistry , vol.18 , Issue.9 , pp. 1222-1232
    • Lee, J.1    Scheraga, H.A.2    Rackovsky, S.3
  • 23
    • 68149125150 scopus 로고    scopus 로고
    • Multiscale characterization of protein conformational ensembles
    • Shehu A, Kavraki LE, Clementi C, Multiscale characterization of protein conformational ensembles, Proteins: Struct Funct Bioinf 76(4):837-851, 2009.
    • (2009) Proteins: Struct. Funct. Bioinf. , vol.76 , Issue.4 , pp. 837-851
    • Shehu, A.1    Kavraki, L.E.2    Clementi, C.3
  • 24
    • 58149277688 scopus 로고    scopus 로고
    • Guiding conformation space search with an all-atom energy potential
    • Brunette TJ, Brock O, Guiding conformation space search with an all-atom energy potential, Proteins: Struct Funct Bioinf 73(4):958-972, 2009.
    • (2009) Proteins: Struct. Funct. Bioinf. , vol.73 , Issue.4 , pp. 958-972
    • Brunette, T.J.1    Brock, O.2
  • 27
    • 39549115231 scopus 로고    scopus 로고
    • Unfolding the fold of cyclic cysteine-rich peptides
    • DOI 10.1110/ps.073142708
    • Shehu A, Kavraki LE, Clementi C, Unfolding the fold of cyclic cysteine-rich peptides, Protein Sci 17(3):482-493, 2008. (Pubitemid 351281549)
    • (2008) Protein Science , vol.17 , Issue.3 , pp. 482-493
    • Shehu, A.1    Kavraki, L.E.2    Clementi, C.3
  • 28
    • 77954063582 scopus 로고    scopus 로고
    • Guiding the search for native-like protein conformations with an ab-initio tree-based exploration
    • Shehu A, Olson B, Guiding the search for native-like protein conformations with an ab-initio tree-based exploration, Int J Robot Res 29(8):1106-11227, 2010.
    • (2010) Int. J. Robot. Res. , vol.29 , Issue.8 , pp. 1106-11227
    • Shehu, A.1    Olson, B.2
  • 29
    • 34547260921 scopus 로고    scopus 로고
    • Ultrafast shape recognition to search compound databases for similar molecular shapes
    • DOI 10.1002/jcc.20681
    • Ballester PJ, Richards G, Ultrafast shape recognition to search compound databases for similar molecular shapes, J Comput Chem 28(10):1711-1723, 2007. (Pubitemid 47146547)
    • (2007) Journal of Computational Chemistry , vol.28 , Issue.10 , pp. 1711-1723
    • Ballester, P.J.1    Richards, W.G.2
  • 30
    • 0037907566 scopus 로고    scopus 로고
    • Reducing the computational complexity of protein folding via fragment folding and assembly
    • DOI 10.1110/ps.0232903
    • Haspel N, Tsai CJ, Wolfson H, Nussinov R, Reducing the computational complexity of protein folding via fragment folding and assembly, Protein Sci 12(6):1177-1187, 2003. (Pubitemid 36597504)
    • (2003) Protein Science , vol.12 , Issue.6 , pp. 1177-1187
    • Haspel, N.1    Tsai, C.-J.2    Wolfson, H.3    Nussinov, R.4
  • 31
    • 0036406112 scopus 로고    scopus 로고
    • Small libraries of protein fragments model native protein structures accurately
    • DOI 10.1016/S0022-2836(02)00942-7
    • Kolodny R, Koehl P, Guibas L, Levitt M, Small libraries of protein fragments model native protein structures accurately, J Mol Biol 323(2):297-307, 2002. (Pubitemid 35283693)
    • (2002) Journal of Molecular Biology , vol.323 , Issue.2 , pp. 297-307
    • Kolodny, R.1    Koehl, P.2    Guibas, L.3    Levitt, M.4
  • 32
    • 0043180474 scopus 로고    scopus 로고
    • PISCES: A protein sequence culling server
    • DOI 10.1093/bioinformatics/btg224
    • Wang G, Dunbrack Jr RL, Pisces: A protein sequence culling server, Bioinformatics 19(12):1589-1591, 2003. (Pubitemid 37038881)
    • (2003) Bioinformatics , vol.19 , Issue.12 , pp. 1589-1591
    • Wang, G.1    Dunbrack Jr., R.L.2
  • 36
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • DOI 10.1006/jmbi.1999.3091
    • Jones DT, Protein secondary structure prediction based on position-specific scoring matrices, J Mol Biol 292(2):195-202, 1999. (Pubitemid 29435759)
    • (1999) Journal of Molecular Biology , vol.292 , Issue.2 , pp. 195-202
    • Jones, D.T.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.