메뉴 건너뛰기




Volumn 36, Issue 6, 2008, Pages 1418-1421

FunHunt: Model selection based on energy landscape characteristics

Author keywords

Energy funnels; Energy landscape; High resolution modelling; Model selection; Protein protein docking; Rosetta

Indexed keywords

AB INITIO CALCULATION; AMINO ACID SEQUENCE; ARTICLE; CLASSIFIER; CLIENT SERVER APPLICATION; COMPLEX FORMATION; HYDROGEN BOND; MACHINE LEARNING; MOLECULAR DOCKING; MOLECULAR MODEL; PREDICTION; PRIORITY JOURNAL; PROCESS DEVELOPMENT; PROCESS OPTIMIZATION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; ALGORITHM; CHEMICAL STRUCTURE; NUCLEOTIDE SEQUENCE; THERMODYNAMICS;

EID: 59149107086     PISSN: 03005127     EISSN: 14708752     Source Type: Journal    
DOI: 10.1042/BST0361418     Document Type: Article
Times cited : (17)

References (22)
  • 1
    • 27344449197 scopus 로고    scopus 로고
    • Progress in modeling of protein structures and interactions
    • Schueler-Furman, O., Wang, C., Bradley, P., Misura, K., and Baker D. (2005) Progress in modeling of protein structures and interactions. Science 310, 638-642
    • (2005) Science , vol.310 , pp. 638-642
    • Schueler-Furman, O.1    Wang, C.2    Bradley, P.3    Misura, K.4    Baker, D.5
  • 2
    • 50649095790 scopus 로고    scopus 로고
    • Macromolecular modeling with Rosetta
    • Das, R. and Baker, D. (2008) Macromolecular modeling with Rosetta. Annu. Rev. Biochem. 77, 363-382
    • (2008) Annu. Rev. Biochem , vol.77 , pp. 363-382
    • Das, R.1    Baker, D.2
  • 3
    • 24944493938 scopus 로고    scopus 로고
    • Toward high-resolution de novo structure prediction for small proteins
    • Bradley, P, Misura, K.M. and Baker, D. (2005) Toward high-resolution de novo structure prediction for small proteins. Science 309, 1868-1871
    • (2005) Science , vol.309 , pp. 1868-1871
    • Bradley, P.1    Misura, K.M.2    Baker, D.3
  • 4
    • 36049029967 scopus 로고    scopus 로고
    • High-resolution structure prediction and the crystallographic phase problem
    • Qian, B., Raman, S., Cas, R., Bradley, P., McCoy, A.J., Read, R.J. and Baker, D. (2007) High-resolution structure prediction and the crystallographic phase problem. Nature 450, 259-264
    • (2007) Nature , vol.450 , pp. 259-264
    • Qian, B.1    Raman, S.2    Cas, R.3    Bradley, P.4    McCoy, A.J.5    Read, R.J.6    Baker, D.7
  • 5
    • 0038161052 scopus 로고    scopus 로고
    • Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
    • Gray, J.J., Moughon, S., Wang, C., Schueler-Furman, O., Kuhlman, B., Rohl, C.A. and Baker, D (2003) Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J. Mol. Biol. 331, 281-299
    • (2003) J. Mol. Biol , vol.331 , pp. 281-299
    • Gray, J.J.1    Moughon, S.2    Wang, C.3    Schueler-Furman, O.4    Kuhlman, B.5    Rohl, C.A.6    Baker, D.7
  • 8
    • 21644459373 scopus 로고    scopus 로고
    • Progress in protein-protein docking: Atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility
    • Schueler-Furman, C., Wang, C. and Baker, D. (2005) Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility. Proteins 60, 187-194
    • (2005) Proteins , vol.60 , pp. 187-194
    • Schueler-Furman, C.1    Wang, C.2    Baker, D.3
  • 9
    • 38949083887 scopus 로고    scopus 로고
    • Funnel hunting in a rough terrain: Learning and discriminating native energy funnels
    • London, N. and Schueler-Furman, O. (2008) Funnel hunting in a rough terrain: learning and discriminating native energy funnels. Structure 16, 269-279
    • (2008) Structure , vol.16 , pp. 269-279
    • London, N.1    Schueler-Furman, O.2
  • 10
    • 59249087136 scopus 로고    scopus 로고
    • Joachims, T. (1999) Making large-scale support vector machine learning practical. In Advances in Kernel Methods: Support Vector Learning (Schölkopf, C , Burges, C. and Smola, A., eds), pp. 169-184, MIT Press, Cambridge, MA
    • Joachims, T. (1999) Making large-scale support vector machine learning practical. In Advances in Kernel Methods: Support Vector Learning (Schölkopf, C , Burges, C. and Smola, A., eds), pp. 169-184, MIT Press, Cambridge, MA
  • 11
    • 36749091035 scopus 로고    scopus 로고
    • Assessing the energy landscape of CAPRI targets by FunHunt
    • London, N. and Schueler-Furman, O. (2007) Assessing the energy landscape of CAPRI targets by FunHunt. Proteins 63, 809-815
    • (2007) Proteins , vol.63 , pp. 809-815
    • London, N.1    Schueler-Furman, O.2
  • 12
    • 0023430366 scopus 로고
    • Monte Carlo-minimization approach to the multiple-minima problem in protein folding
    • Li, Z. and Scheraga, H.A. (1987) Monte Carlo-minimization approach to the multiple-minima problem in protein folding. Proc. Natl. Acad. Sci. U.S.A. 84, 6611-6615
    • (1987) Proc. Natl. Acad. Sci. U.S.A , vol.84 , pp. 6611-6615
    • Li, Z.1    Scheraga, H.A.2
  • 13
    • 17744364070 scopus 로고    scopus 로고
    • Improved side-chain modeling for protein-protein docking
    • Wang, C., Schueler-Furman, O. and Baker, D. (2005) Improved side-chain modeling for protein-protein docking. Protein Sci 14, 1328-1339
    • (2005) Protein Sci , vol.14 , pp. 1328-1339
    • Wang, C.1    Schueler-Furman, O.2    Baker, D.3
  • 14
    • 0036161259 scopus 로고    scopus 로고
    • Gene selection for cancer classification using support vector machines
    • Guyon, I., Weston, J., Barnhill, S. and Vapnilk, V. (2002) Gene selection for cancer classification using support vector machines. Machine Learning 46, 389-422
    • (2002) Machine Learning , vol.46 , pp. 389-422
    • Guyon, I.1    Weston, J.2    Barnhill, S.3    Vapnilk, V.4
  • 16
    • 0035889692 scopus 로고    scopus 로고
    • New insights into the mechanism of protein-protein association
    • Selzer, T. and Schreibeir, C (2001) New insights into the mechanism of protein-protein association. Proteins 45, 190-198
    • (2001) Proteins , vol.45 , pp. 190-198
    • Selzer, T.1    Schreibeir, C.2
  • 18
    • 47349119911 scopus 로고    scopus 로고
    • Discrimination of near-native structures in protein-protein docking by testing the stability of local minima
    • Kozakov, D., Schuelef-Furman, O. and Vajda, S. (2008) Discrimination of near-native structures in protein-protein docking by testing the stability of local minima. Proteins 72, 993-1004
    • (2008) Proteins , vol.72 , pp. 993-1004
    • Kozakov, D.1    Schuelef-Furman, O.2    Vajda, S.3
  • 19
    • 2542445427 scopus 로고    scopus 로고
    • ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information
    • Glaser, F., Pupko, T., Paz, I., Bell, R.E., Bechor-Shental, D., Martz, E. and Ben-Tal, N. (2003) ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics 19, 163-164
    • (2003) Bioinformatics , vol.19 , pp. 163-164
    • Glaser, F.1    Pupko, T.2    Paz, I.3    Bell, R.E.4    Bechor-Shental, D.5    Martz, E.6    Ben-Tal, N.7
  • 20
    • 1842526090 scopus 로고    scopus 로고
    • ProMate a structure based prediction program to identify the location of protein-pfotein binding sites
    • Neuvirth, H., Raz, R. and Schreiber, G. (2004) ProMate a structure based prediction program to identify the location of protein-pfotein binding sites. J. Mol. Biol. 338, 181-199
    • (2004) J. Mol. Biol , vol.338 , pp. 181-199
    • Neuvirth, H.1    Raz, R.2    Schreiber, G.3
  • 21
    • 0028304962 scopus 로고
    • Satisfying hydrogen bonding potential in proteins
    • McDonald, I.K. and Thornton, J.M. (1994) Satisfying hydrogen bonding potential in proteins. J. Mol. Biol. 238, 777-793
    • (1994) J. Mol. Biol , vol.238 , pp. 777-793
    • McDonald, I.K.1    Thornton, J.M.2
  • 22
    • 12944257228 scopus 로고    scopus 로고
    • The ConSurf-HSSP database: The mapping of evolutionary conservation among homologs onto PDB structures
    • Glaser, F., Rosenberg, Y., Kessel, A., Puplko, T. and Ben-Tal, N. (2005) The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures. Proteins 58, 610-617
    • (2005) Proteins , vol.58 , pp. 610-617
    • Glaser, F.1    Rosenberg, Y.2    Kessel, A.3    Puplko, T.4    Ben-Tal, N.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.