메뉴 건너뛰기




Volumn 87 LNICST, Issue , 2012, Pages 249-263

Enhancing sampling of the conformational space near the protein native state

Author keywords

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

Indexed keywords

CONFORMATIONAL ENSEMBLE; CONFORMATIONAL SPACE; ENERGY SURFACE; HIGH-DIMENSIONAL; LOW-ENERGY CONFORMATIONS; NATIVE CONFORMATION; NATIVE STATE; PROBABILISTIC SEARCH; PROTEIN FUNCTIONS; PROTEIN MOLECULES; SEARCH ALGORITHMS; STRUCTURAL DIVERSITY; THREE-DIMENSIONAL STRUCTURE; TREE-BASED;

EID: 84869595578     PISSN: 18678211     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-3-642-32615-8_26     Document Type: Conference Paper
Times cited : (3)

References (39)
  • 2
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • Anfinsen, C.B.: 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
  • 3
    • 34547260921 scopus 로고    scopus 로고
    • Ultrafast shape recognition to search compound databases for similar molecular shapes
    • Ballester, P.J., Richards, G.: Ultrafast shape recognition to search compound databases for similar molecular shapes. J. Comput. Chem. 28(10), 1711-1723 (2007)
    • (2007) J. Comput. Chem. , vol.28 , Issue.10 , pp. 1711-1723
    • Ballester, P.J.1    Richards, G.2
  • 5
    • 0036968925 scopus 로고    scopus 로고
    • De novo prediction of three-dimensional structures for major protein families
    • Bonneau, R., Baker, D.: De novo prediction of three-dimensional structures for major protein families. J. Mol. Biol. 322(1), 65-78 (2002)
    • (2002) J. Mol. Biol. , vol.322 , Issue.1 , pp. 65-78
    • Bonneau, R.1    Baker, D.2
  • 6
    • 24944493938 scopus 로고    scopus 로고
    • Toward high-resolution de novo structure prediction for small proteins
    • Bradley, P., Misura, K.M.S., Baker, D.: 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
  • 7
    • 58149277688 scopus 로고    scopus 로고
    • Guiding conformation space search with an all-atom energy potential
    • Brunette, T.J., 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
  • 8
    • 0042511005 scopus 로고    scopus 로고
    • A graph-theory algorithm for rapid protein side chain prediction
    • Canutescu, A.A., Shelenkov, A.A., Dunbrack Jr., R.L.: A graph-theory algorithm for rapid protein side chain prediction. Protein Sci. 12(9), 2001-2014 (2003)
    • (2003) Protein Sci. , vol.12 , Issue.9 , pp. 2001-2014
    • Canutescu, A.A.1    Shelenkov, A.A.2    Dunbrack Jr., R.L.3
  • 10
    • 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. Opinion Struct. Biol. 18, 10-15 (2008)
    • (2008) Curr. Opinion Struct. Biol. , vol.18 , pp. 10-15
    • Clementi, C.1
  • 12
    • 1842298212 scopus 로고    scopus 로고
    • From levinthal to pathways to funnels
    • Dill, K.A., Chan, H.S.: 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
  • 15
    • 0026320866 scopus 로고
    • The energy landscapes and motion on proteins
    • Frauenfelder, H., Sligar, S.G., Wolynes, P.G.: 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
  • 16
    • 0037907566 scopus 로고    scopus 로고
    • Reducing the computational complexity of protein folding via fragment folding and assembly
    • Haspel, N., Tsai, C., Wolfson, H., Nussinov, R.: Reducing the computational complexity of protein folding via fragment folding and assembly. Protein Sci. 12(6), 1177-1187 (2003)
    • (2003) Protein Sci. , vol.12 , Issue.6 , pp. 1177-1187
    • Haspel, N.1    Tsai, C.2    Wolfson, H.3    Nussinov, R.4
  • 17
    • 34447515841 scopus 로고    scopus 로고
    • From coarse-grain to all-atom: Towards multiscale analysis of protein landscapes
    • Heath, A.P., Kavraki, L.E., Clementi, C.: From coarse-grain to all-atom: Towards multiscale analysis of protein landscapes. Proteins: Struct. Funct. Bioinf. 68(3), 646-661 (2007)
    • (2007) Proteins: Struct. Funct. Bioinf. , vol.68 , Issue.3 , pp. 646-661
    • Heath, A.P.1    Kavraki, L.E.2    Clementi, C.3
  • 18
    • 27744480205 scopus 로고    scopus 로고
    • Structural biology: Proteins flex to function
    • Huang, Y.J., Montellione, G.T.: Structural biology: Proteins flex to function. Nature 438(7064), 36-37 (2005)
    • (2005) Nature , vol.438 , Issue.7064 , pp. 36-37
    • Huang, Y.J.1    Montellione, G.T.2
  • 19
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones, D.T.: Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292(2), 195-202 (1999)
    • (1999) J. Mol. Biol. , vol.292 , Issue.2 , pp. 195-202
    • Jones, D.T.1
  • 20
    • 0036406112 scopus 로고    scopus 로고
    • Small libraries of protein fragments model native protein structures accurately
    • 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)
    • (2002) J. Mol. Biol. , vol.323 , Issue.2 , pp. 297-307
    • Kolodny, R.1    Koehl, P.2    Guibas, L.3    Levitt, M.4
  • 21
    • 1042298843 scopus 로고    scopus 로고
    • Computational design of protein-protein interactions
    • Kortemme, T., Baker, D.: Computational design of protein-protein interactions. Curr. Opinion Struct. Biol. 8(1), 91-97 (2004)
    • (2004) Curr. Opinion Struct. Biol. , vol.8 , Issue.1 , pp. 91-97
    • Kortemme, T.1    Baker, D.2
  • 22
    • 53849129958 scopus 로고    scopus 로고
    • Workspace-based connectivity oracle: An adaptive sampling strategy for PRM planning
    • Kurniawati, H., Hsu, D.: Workspace-based connectivity oracle: An adaptive sampling strategy for PRM planning. In: WAFR. Springer Tracts in Advanced Robotics. vol. 47, pp. 35-51 (2006)
    • (2006) WAFR. Springer Tracts in Advanced Robotics , vol.47 , pp. 35-51
    • Kurniawati, H.1    Hsu, D.2
  • 23
    • 33747610281 scopus 로고    scopus 로고
    • Motion planning in the presence of drift, underactuation and discrete system changes
    • Ladd, A.M., Kavraki, L.E.: Motion planning in the presence of drift, underactuation and discrete system changes. In: Robotics: Sci. and Syst., pp. 233-241 (2005)
    • (2005) Robotics: Sci. and Syst. , pp. 233-241
    • Ladd, A.M.1    Kavraki, L.E.2
  • 24
    • 36448988254 scopus 로고    scopus 로고
    • Predicting protein function from sequence and structure
    • Lee, D., Redfern, O., Orengo, C.: Predicting protein function from sequence and structure. Nat. Rev. Mol. Cell Biol. 8(12), 995-1005 (2007)
    • (2007) Nat. Rev. Mol. Cell Biol. , vol.8 , Issue.12 , pp. 995-1005
    • Lee, D.1    Redfern, O.2    Orengo, C.3
  • 25
    • 0001176785 scopus 로고    scopus 로고
    • New optimization method for conformational energy calculations on polypeptides: Conformational space annealing
    • Lee, J., Scheraga, H.A., Rackovsky, S.: New optimization method for conformational energy calculations on polypeptides: Conformational space annealing. J. Comput. Chem. 18(9), 1222-1232 (1997)
    • (1997) J. Comput. Chem. , vol.18 , Issue.9 , pp. 1222-1232
    • Lee, J.1    Scheraga, H.A.2    Rackovsky, S.3
  • 26
    • 0032146482 scopus 로고    scopus 로고
    • Conformational analysis of the 20-residue membrane-bound portion of melittin by conformational space annealing
    • Lee, J., Scheraga, H.A., Rackovsky, S.: Conformational analysis of the 20-residue membrane-bound portion of melittin by conformational space annealing. Biopolymers 46(2), 103-115 (1998)
    • (1998) Biopolymers , vol.46 , Issue.2 , pp. 103-115
    • Lee, J.1    Scheraga, H.A.2    Rackovsky, S.3
  • 27
    • 34249891085 scopus 로고    scopus 로고
    • Protein structure initiative: Geeting into gear
    • Matthews, B.W.: Protein structure initiative: geeting into gear. Nat. Struct. Biol. & Mol. Biol. 14(6), 459-460 (2007)
    • (2007) Nat. Struct. Biol. & Mol. Biol. , vol.14 , Issue.6 , pp. 459-460
    • Matthews, B.W.1
  • 28
    • 51649128820 scopus 로고    scopus 로고
    • Discrete search leading continuous exploration for kinodynamicmotion planning
    • Atlanta, GA, USA
    • Plaku, E., Kavraki, L., Vardi,M.: Discrete search leading continuous exploration for kinodynamicmotion planning. In: Robotics: Sci. and Syst., Atlanta, GA, USA (2007)
    • (2007) Robotics: Sci. and Syst.
    • Plaku, E.1    Kavraki, L.2    Vardi, M.3
  • 30
    • 0036458038 scopus 로고    scopus 로고
    • On delaying collision checking in PRM planning: Application to multi-robot coordination
    • Sánchez, G., Latombe, J.-C.: 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
  • 32
    • 39549115231 scopus 로고    scopus 로고
    • Unfolding the fold of cyclic cysteine-rich peptides
    • Shehu, A., Kavraki, L.E., Clementi, C.: 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
  • 33
    • 68149125150 scopus 로고    scopus 로고
    • Multiscale characterization of protein conformational ensembles
    • Shehu, A., Kavraki, L.E., 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
  • 34
    • 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
  • 35
    • 57249105450 scopus 로고    scopus 로고
    • Planning among movable obstacles with artificial constraints
    • Stilman, M., Kuffner, J.J.: 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
  • 36
    • 29144459602 scopus 로고    scopus 로고
    • Using workspace information as a guide to non-uniform sampling in probabilistic roadmap planners
    • van den Berg, J.P., Overmars, M.H.: Using workspace information as a guide to non-uniform sampling in probabilistic roadmap planners. Int. J. Robot. Res. 24(12), 1055-1071 (2005)
    • (2005) Int. J. Robot. Res. , vol.24 , Issue.12 , pp. 1055-1071
    • Van Den Berg, J.P.1    Overmars, M.H.2
  • 37
    • 0043180474 scopus 로고    scopus 로고
    • Pisces: A protein sequence culling server
    • Wang, G., Dunbrack, R.L.: Pisces: a protein sequence culling server. Bioinformatics 19(12), 1589-1591 (2003)
    • (2003) Bioinformatics , vol.19 , Issue.12 , pp. 1589-1591
    • Wang, G.1    Dunbrack, R.L.2
  • 38
    • 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: Sci. and Syst., Cambridge, MA, pp. 97-104 (2005)
    • (2005) Robotics: Sci. and Syst. , pp. 97-104
    • Yang, Y.1    Brock, O.2
  • 39
    • 34249777526 scopus 로고    scopus 로고
    • Eris: An automated estimator of protein stability
    • Yin, S., Ding, F., Dokholyan, N.V.: Eris: an automated estimator of protein stability. Nat. Methods 4(6), 466-467 (2007)
    • (2007) Nat. Methods , vol.4 , Issue.6 , pp. 466-467
    • Yin, S.1    Ding, F.2    Dokholyan, N.V.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.