메뉴 건너뛰기




Volumn 79, Issue 8, 2011, Pages 2467-2474

A machine learning approach for the prediction of protein surface loop flexibility

Author keywords

B factor; Backbone; Flexibility; Loop; Protein; Random Forest; SVM

Indexed keywords

PROTEIN CDC42; PROTEIN P67; RAC PROTEIN; RAN PROTEIN; RAS PROTEIN;

EID: 79960075532     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.23070     Document Type: Article
Times cited : (9)

References (37)
  • 1
    • 36749006579 scopus 로고    scopus 로고
    • Docking and scoring protein complexes: CAPRI 3rd Edition
    • Lensink MF, Mendez R, Wodak SJ. Docking and scoring protein complexes: CAPRI 3rd Edition. Proteins 2007; 69: 704-718.
    • (2007) Proteins , vol.69 , pp. 704-718
    • Lensink, M.F.1    Mendez, R.2    Wodak, S.J.3
  • 2
    • 77957948556 scopus 로고    scopus 로고
    • Blind predictions of protein interfaces by docking calculations in CAPRI
    • Lensink MF, Wodak SJ. Blind predictions of protein interfaces by docking calculations in CAPRI. Proteins 2010; 78: 3085-3095.
    • (2010) Proteins , vol.78 , pp. 3085-3095
    • Lensink, M.F.1    Wodak, S.J.2
  • 3
    • 0027160197 scopus 로고
    • Backbone-dependent rotamer library for proteins. Application to side-chain prediction
    • Dunbrack RL, Jr, Karplus M. Backbone-dependent rotamer library for proteins. Application to side-chain prediction. J Mol Biol 1993; 230: 543-574.
    • (1993) J Mol Biol , vol.230 , pp. 543-574
    • Dunbrack Jr, R.L.1    Karplus, M.2
  • 4
    • 0031576989 scopus 로고    scopus 로고
    • Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool
    • Bower MJ, Cohen FE, Dunbrack RL, Jr. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. J Mol Biol 1997; 267: 1268-1282.
    • (1997) J Mol Biol , vol.267 , pp. 1268-1282
    • Bower, M.J.1    Cohen, F.E.2    Dunbrack Jr, R.L.3
  • 5
    • 0036173727 scopus 로고    scopus 로고
    • On residues in the disallowed region of the Ramachandran map
    • Pal D, Chakrabarti P. On residues in the disallowed region of the Ramachandran map. Biopolymers 2002; 63: 195-206.
    • (2002) Biopolymers , vol.63 , pp. 195-206
    • Pal, D.1    Chakrabarti, P.2
  • 6
    • 0032718454 scopus 로고    scopus 로고
    • Skewed distribution of protein secondary structure contents over the conformational triangle
    • Zhang CT, Zhang R. Skewed distribution of protein secondary structure contents over the conformational triangle. Protein Eng 1999; 12: 807-810.
    • (1999) Protein Eng , vol.12 , pp. 807-810
    • Zhang, C.T.1    Zhang, R.2
  • 7
    • 0003187567 scopus 로고    scopus 로고
    • The atomic structure of protein-protein recognition sites
    • Lo Conte L, Chothia C, Janin J. The atomic structure of protein-protein recognition sites. J Mol Biol 1999; 285: 2177-2198.
    • (1999) J Mol Biol , vol.285 , pp. 2177-2198
    • Lo Conte, L.1    Chothia, C.2    Janin, J.3
  • 8
    • 33645961330 scopus 로고    scopus 로고
    • Flexible protein-protein docking
    • Bonvin AM. Flexible protein-protein docking. Curr Opin Struct Biol 2006; 16: 194-200.
    • (2006) Curr Opin Struct Biol , vol.16 , pp. 194-200
    • Bonvin, A.M.1
  • 9
    • 44949083561 scopus 로고    scopus 로고
    • Ordered conformational change in the protein backbone: prediction of conformationally variable positions from sequence and low-resolution structural data
    • Kuznetsov IB. Ordered conformational change in the protein backbone: prediction of conformationally variable positions from sequence and low-resolution structural data. Proteins 2008; 72(1): 74-87.
    • (2008) Proteins , vol.72 , Issue.1 , pp. 74-87
    • Kuznetsov, I.B.1
  • 11
    • 34548861782 scopus 로고    scopus 로고
    • Protein-protein docking with backbone flexibility
    • Wang C, Bradley P, Baker D. Protein-protein docking with backbone flexibility. J Mol Biol 2007; 373: 503-519.
    • (2007) J Mol Biol , vol.373 , pp. 503-519
    • Wang, C.1    Bradley, P.2    Baker, D.3
  • 12
    • 77951232176 scopus 로고    scopus 로고
    • FiberDock: flexible induced-fit backbone refinement in molecular docking
    • Mashiach E, Nussinov R, Wolfson HJ. FiberDock: flexible induced-fit backbone refinement in molecular docking. Proteins 2010; 78: 1503-1519.
    • (2010) Proteins , vol.78 , pp. 1503-1519
    • Mashiach, E.1    Nussinov, R.2    Wolfson, H.J.3
  • 13
    • 33644843079 scopus 로고    scopus 로고
    • Accounting for loop flexibility during protein-protein docking
    • Bastard K, Prevost C, Zacharias M. Accounting for loop flexibility during protein-protein docking. Proteins 2006; 62: 956-969.
    • (2006) Proteins , vol.62 , pp. 956-969
    • Bastard, K.1    Prevost, C.2    Zacharias, M.3
  • 14
    • 33845703344 scopus 로고    scopus 로고
    • What is a support vector machine?
    • Noble WS. What is a support vector machine? Nat Biotechnol 2006; 24: 1565-1567.
    • (2006) Nat Biotechnol , vol.24 , pp. 1565-1567
    • Noble, W.S.1
  • 16
    • 79960101596 scopus 로고    scopus 로고
    • Dunbrack RL. S2C: a database correlating sequence and atomic coordinate numbering in the Protein Data Bank. Available at: Accessed on 11 Oct, 2007.
    • Wang G, Arthur JW, Dunbrack RL. S2C: a database correlating sequence and atomic coordinate numbering in the Protein Data Bank. Available at: Accessed on 11 Oct, 2007.
    • Wang, G.1    Arthur, J.W.2
  • 17
    • 0029619259 scopus 로고
    • Knowledge-based protein secondary structure assignment
    • Frishman D, Argos P. Knowledge-based protein secondary structure assignment. Proteins 1995; 23: 566-579.
    • (1995) Proteins , vol.23 , pp. 566-579
    • Frishman, D.1    Argos, P.2
  • 18
    • 79960077162 scopus 로고
    • NACCESS computer program. Department of Biochemistry and Molecular Biology, University College of London, UK. Program is available at: manchester.ac.uk/naccess/.
    • Hubbard SJ, Thornton JM. 1993. NACCESS computer program. Department of Biochemistry and Molecular Biology, University College of London, UK. Program is available at: manchester.ac.uk/naccess/.
    • (1993)
    • Hubbard, S.J.1    Thornton, J.M.2
  • 20
    • 79960098600 scopus 로고    scopus 로고
    • LIBSVM: a library for support vector machines. Program is available at
    • Chih-Chung C, Chih-Jen L. LIBSVM: a library for support vector machines. 2001. Program is available at:
    • (2001)
    • Chih-Chung, C.1    Chih-Jen, L.2
  • 21
    • 0025912338 scopus 로고
    • Molecular recognition. Conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors
    • Hubbard SJ, Campbell SF, Thornton JM. Molecular recognition. Conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors. J Mol Biol 1991; 220: 507-530.
    • (1991) J Mol Biol , vol.220 , pp. 507-530
    • Hubbard, S.J.1    Campbell, S.F.2    Thornton, J.M.3
  • 23
    • 0029978353 scopus 로고    scopus 로고
    • Analysis of main chain torsion angles in proteins: prediction of NMR coupling constants for native and random coil conformations
    • Smith LJ, Bolin KA, Schwalbe H, MacArthur MW, Thornton JM, Dobson CM. Analysis of main chain torsion angles in proteins: prediction of NMR coupling constants for native and random coil conformations. J Mol Biol 1996; 255: 494-506.
    • (1996) J Mol Biol , vol.255 , pp. 494-506
    • Smith, L.J.1    Bolin, K.A.2    Schwalbe, H.3    MacArthur, M.W.4    Thornton, J.M.5    Dobson, C.M.6
  • 24
    • 24644449168 scopus 로고    scopus 로고
    • Main-chain conformational tendencies of amino acids
    • Anderson RJ, Weng Z, Campbell RK, Jiang X. Main-chain conformational tendencies of amino acids. Proteins 2005; 60: 679-689.
    • (2005) Proteins , vol.60 , pp. 679-689
    • Anderson, R.J.1    Weng, Z.2    Campbell, R.K.3    Jiang, X.4
  • 25
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • Breiman L. Random forests. Machine Learn 2001; 45: 5-32.
    • (2001) Machine Learn , vol.45 , pp. 5-32
    • Breiman, L.1
  • 26
    • 0345040873 scopus 로고    scopus 로고
    • Classification and regression by randomForest
    • Liaw A, Wiener M. Classification and regression by randomForest. R News 2002; 2: 18-22.
    • (2002) R News , vol.2 , pp. 18-22
    • Liaw, A.1    Wiener, M.2
  • 27
    • 34047138318 scopus 로고    scopus 로고
    • Combining {SVM}s with various feature selection strategies
    • In: Guyon ISG,Nikravesh M,Zadeh L, editors. New York: Springer
    • Chen YW, Lin CJ. Combining {SVM}s with various feature selection strategies. In: Guyon ISG, Nikravesh M, Zadeh L, editors. Feature extraction, foundations and applications. New York: Springer; 2006. p. 315-323.
    • (2006) Feature extraction, foundations and applications , pp. 315-323
    • Chen, Y.W.1    Lin, C.J.2
  • 29
    • 77957944014 scopus 로고    scopus 로고
    • Protein-protein docking benchmark version 4.0
    • Hwang H, Vreven T, Janin J, Weng Z. Protein-protein docking benchmark version 4.0. Proteins 2010; 78: 3111-3114.
    • (2010) Proteins , vol.78 , pp. 3111-3114
    • Hwang, H.1    Vreven, T.2    Janin, J.3    Weng, Z.4
  • 30
    • 0025117674 scopus 로고
    • Molecular switch for signal transduction: structural differences between active and inactive forms of protooncogenic ras proteins
    • Milburn MV, Tong L, deVos AM, Brunger A, Yamaizumi Z, Nishimura S, Kim SH. Molecular switch for signal transduction: structural differences between active and inactive forms of protooncogenic ras proteins. Science 1990; 247: 939-945.
    • (1990) Science , vol.247 , pp. 939-945
    • Milburn, M.V.1    Tong, L.2    deVos, A.M.3    Brunger, A.4    Yamaizumi, Z.5    Nishimura, S.6    Kim, S.H.7
  • 32
    • 0036789949 scopus 로고    scopus 로고
    • Ras and relatives-job sharing and networking keep an old family together
    • Ehrhardt A, Ehrhardt GR, Guo X, Schrader JW. Ras and relatives-job sharing and networking keep an old family together. Exp Hematol 2002; 30: 1089-1106.
    • (2002) Exp Hematol , vol.30 , pp. 1089-1106
    • Ehrhardt, A.1    Ehrhardt, G.R.2    Guo, X.3    Schrader, J.W.4
  • 33
    • 77957934896 scopus 로고    scopus 로고
    • Docking and scoring protein interactions: CAPRI 2009
    • Lensink MF, Wodak SJ. Docking and scoring protein interactions: CAPRI 2009. Proteins 2010; 78: 3073-3084.
    • (2010) Proteins , vol.78 , pp. 3073-3084
    • Lensink, M.F.1    Wodak, S.J.2
  • 36
    • 77957951743 scopus 로고    scopus 로고
    • Performance of ZDOCK and ZRANK in CAPRI rounds 13-19
    • Hwang H, Vreven T, Pierce BG, Hung JH, Weng Z. Performance of ZDOCK and ZRANK in CAPRI rounds 13-19. Proteins 2010; 78: 3104-3110.
    • (2010) Proteins , vol.78 , pp. 3104-3110
    • Hwang, H.1    Vreven, T.2    Pierce, B.G.3    Hung, J.H.4    Weng, Z.5
  • 37
    • 33747150197 scopus 로고    scopus 로고
    • Protein binding site prediction using an empirical scoring function
    • Liang S, Zhang C, Liu S, Zhou Y. Protein binding site prediction using an empirical scoring function. Nucleic Acids Res 2006; 34: 3698-3707.
    • (2006) Nucleic Acids Res , vol.34 , pp. 3698-3707
    • Liang, S.1    Zhang, C.2    Liu, S.3    Zhou, Y.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.