메뉴 건너뛰기




Volumn 68, Issue 1, 2007, Pages 187-194

Identification of near-native structures by clustering protein docking conformations

Author keywords

Docking decoy; Docking meta server; Fast fourier transformation; Protein structure clustering; Protein protein docking; TM score

Indexed keywords

PROTEIN;

EID: 34249912111     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21442     Document Type: Article
Times cited : (59)

References (31)
  • 1
    • 0026572775 scopus 로고
    • Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques
    • Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem AA, Aflalo C, Vakser IA. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci USA 1992;89:2195-2199.
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 2195-2199
    • Katchalski-Katzir, E.1    Shariv, I.2    Eisenstein, M.3    Friesem, A.A.4    Aflalo, C.5    Vakser, I.A.6
  • 2
    • 0038185277 scopus 로고    scopus 로고
    • A novel shape complementarity scoring function for protein-protein docking
    • Chen R, Weng Z. A novel shape complementarity scoring function for protein-protein docking. Proteins 2003;51:397-408.
    • (2003) Proteins , vol.51 , pp. 397-408
    • Chen, R.1    Weng, Z.2
  • 3
    • 0037093643 scopus 로고    scopus 로고
    • Docking unbound proteins using shape complementarity, desolvation, and electrostatics
    • Chen R, Weng Z. Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins 2002;47:281-294.
    • (2002) Proteins , vol.47 , pp. 281-294
    • Chen, R.1    Weng, Z.2
  • 4
    • 0031565730 scopus 로고    scopus 로고
    • Modelling protein docking using shape complementarity, electrostatics and biochemical information
    • Gabb HA, Jackson RM, Sternberg MJ. Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol 1997;272:106-120.
    • (1997) J Mol Biol , vol.272 , pp. 106-120
    • Gabb, H.A.1    Jackson, R.M.2    Sternberg, M.J.3
  • 5
    • 21644458085 scopus 로고    scopus 로고
    • Development and testing of an automated approach to protein docking
    • Tovchigrechko A, Vakser IA. Development and testing of an automated approach to protein docking. Proteins 2005;60:296-301.
    • (2005) Proteins , vol.60 , pp. 296-301
    • Tovchigrechko, A.1    Vakser, I.A.2
  • 6
    • 0242299200 scopus 로고    scopus 로고
    • RDOCK: Refinement of rigid-body protein docking predictions
    • Li L, Chen R, Weng Z. RDOCK: refinement of rigid-body protein docking predictions. Proteins 2003;53:693-707.
    • (2003) Proteins , vol.53 , pp. 693-707
    • Li, L.1    Chen, R.2    Weng, Z.3
  • 7
    • 0032512619 scopus 로고    scopus 로고
    • Rapid refinement of protein interfaces incorporating solvation: Application to the docking problem
    • Jackson RM, Gabb HA, Sternberg MJ. Rapid refinement of protein interfaces incorporating solvation: application to the docking problem. J Mol Biol 1998;276:265-285.
    • (1998) J Mol Biol , vol.276 , pp. 265-285
    • Jackson, R.M.1    Gabb, H.A.2    Sternberg, M.J.3
  • 8
    • 0033562633 scopus 로고    scopus 로고
    • Use of pair potentials across protein interfaces in screening predicted docked complexes
    • Mount G, Gabb HA, Sternberg MJ. Use of pair potentials across protein interfaces in screening predicted docked complexes. Proteins 1999;35:364-373.
    • (1999) Proteins , vol.35 , pp. 364-373
    • Mount, G.1    Gabb, H.A.2    Sternberg, M.J.3
  • 9
    • 0032981961 scopus 로고    scopus 로고
    • Free energy landscapes of encounter complexes in protein-protein association
    • Camacho CJ, Weng Z, Vajda S, DeLisi C. Free energy landscapes of encounter complexes in protein-protein association. Biophys J 1999;76:1166-1178.
    • (1999) Biophys J , vol.76 , pp. 1166-1178
    • Camacho, C.J.1    Weng, Z.2    Vajda, S.3    DeLisi, C.4
  • 10
    • 0032530578 scopus 로고    scopus 로고
    • Clustering of low-energy conformations near the native structures of small proteins
    • Shortle D, Simons KT, Baker D. Clustering of low-energy conformations near the native structures of small proteins. Proc Natl Acad Sci USA 1998;95:11158-11162.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 11158-11162
    • Shortle, D.1    Simons, K.T.2    Baker, D.3
  • 11
    • 1942519275 scopus 로고    scopus 로고
    • SPICKER: A clustering approach to identify near-native protein folds
    • Zhang Y, Skolnick J. SPICKER: a clustering approach to identify near-native protein folds. J Comput Chem 2004;25:865-871.
    • (2004) J Comput Chem , vol.25 , pp. 865-871
    • Zhang, Y.1    Skolnick, J.2
  • 12
    • 0030248996 scopus 로고    scopus 로고
    • Low-resolution docking: Prediction of complexes for underdetermined structures
    • Vakser IA. Low-resolution docking: prediction of complexes for underdetermined structures. Biopolymers 1996;39:455-464.
    • (1996) Biopolymers , vol.39 , pp. 455-464
    • Vakser, I.A.1
  • 13
    • 0033587727 scopus 로고    scopus 로고
    • A systematic study of low-resolution recognition in protein-protein complexes
    • Vakser IA, Matar OG, Lam CF. A systematic study of low-resolution recognition in protein-protein complexes. Proc Natl Acad Sci USA 1999;96:8477-8482.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 8477-8482
    • Vakser, I.A.1    Matar, O.G.2    Lam, C.F.3
  • 14
    • 0038359612 scopus 로고    scopus 로고
    • Finding needles in haystacks: Reranking DOT results by using shape complementarity, cluster analysis, and biological information
    • Law DS, Ten Eyck LF, Katzenelson O, Tsigelny I, Roberts VA, Pique ME, Mitchell JC. Finding needles in haystacks: Reranking DOT results by using shape complementarity, cluster analysis, and biological information. Proteins 2003;52:33-40.
    • (2003) Proteins , vol.52 , pp. 33-40
    • Law, D.S.1    Ten Eyck, L.F.2    Katzenelson, O.3    Tsigelny, I.4    Roberts, V.A.5    Pique, M.E.6    Mitchell, J.C.7
  • 16
    • 0038359596 scopus 로고    scopus 로고
    • Successful discrimination of protein interactions
    • Camacho CJ, Gatchell DW. Successful discrimination of protein interactions. Proteins 2003;52:92-97.
    • (2003) Proteins , vol.52 , pp. 92-97
    • Camacho, C.J.1    Gatchell, D.W.2
  • 17
    • 3242877815 scopus 로고    scopus 로고
    • Comeau SR, Gatchell DW, Vajda S, Camacho CJ. ClusPro: a fully automated algorithm for protein-protein docking. Nucleic Acids Res 2004;32(Web Server issue):W96-W99.
    • Comeau SR, Gatchell DW, Vajda S, Camacho CJ. ClusPro: a fully automated algorithm for protein-protein docking. Nucleic Acids Res 2004;32(Web Server issue):W96-W99.
  • 18
    • 0345832301 scopus 로고    scopus 로고
    • ClusPro: An automated docking and discrimination method for the prediction of protein complexes
    • Comeau SR, Gatchell DW, Vajda S, Camacho CJ. ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics 2004;20:45-50.
    • (2004) Bioinformatics , vol.20 , pp. 45-50
    • Comeau, S.R.1    Gatchell, D.W.2    Vajda, S.3    Camacho, C.J.4
  • 19
    • 21644469377 scopus 로고    scopus 로고
    • Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures
    • Mendez R, Leplae R, Lensink MF, Wodak SJ. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins 2005;60:150-169.
    • (2005) Proteins , vol.60 , pp. 150-169
    • Mendez, R.1    Leplae, R.2    Lensink, M.F.3    Wodak, S.J.4
  • 20
    • 23244436580 scopus 로고    scopus 로고
    • Optimal clustering for detecting near-native conformations in protein docking
    • Kozakov D, Clodfelter KH, Vajda S, Camacho CJ. Optimal clustering for detecting near-native conformations in protein docking. Biophys J 2005;89:867-875.
    • (2005) Biophys J , vol.89 , pp. 867-875
    • Kozakov, D.1    Clodfelter, K.H.2    Vajda, S.3    Camacho, C.J.4
  • 21
    • 0037624841 scopus 로고    scopus 로고
    • 3D-SHOTGUN: A novel, cooperative, fold-recognition meta-predictor
    • Fischer D. 3D-SHOTGUN: a novel, cooperative, fold-recognition meta-predictor. Proteins 2003;51:434-441.
    • (2003) Proteins , vol.51 , pp. 434-441
    • Fischer, D.1
  • 22
    • 0038386050 scopus 로고    scopus 로고
    • 3D-Jury: A simple approach to improve protein structure predictions
    • Ginalski K, Elofsson A, Fischer D, Rychlewski L. 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 2003;19:1015-1018.
    • (2003) Bioinformatics , vol.19 , pp. 1015-1018
    • Ginalski, K.1    Elofsson, A.2    Fischer, D.3    Rychlewski, L.4
  • 23
    • 0034780030 scopus 로고    scopus 로고
    • Peons: A neural-network-based consensus predictor that improves fold recognition
    • Lundstrom J, Rychlewski L, Bujnicki J, Elofsson A. Peons: a neural-network-based consensus predictor that improves fold recognition. Protein Sci 2001;10:2354-2362.
    • (2001) Protein Sci , vol.10 , pp. 2354-2362
    • Lundstrom, J.1    Rychlewski, L.2    Bujnicki, J.3    Elofsson, A.4
  • 24
    • 33646817694 scopus 로고    scopus 로고
    • Scoring a diverse set of high-quality docked conformations: A metascore based on electrostatic and desolvation interactions
    • Camacho CJ, Ma H, Champ PC. Scoring a diverse set of high-quality docked conformations: a metascore based on electrostatic and desolvation interactions. Proteins 2006;63:868-877.
    • (2006) Proteins , vol.63 , pp. 868-877
    • Camacho, C.J.1    Ma, H.2    Champ, P.C.3
  • 26
    • 0038526303 scopus 로고    scopus 로고
    • ZDOCK: An initial-stage protein-docking algorithm
    • Chen R, Li L, Weng Z. ZDOCK: an initial-stage protein-docking algorithm. Proteins 2003;52:80-87.
    • (2003) Proteins , vol.52 , pp. 80-87
    • Chen, R.1    Li, L.2    Weng, Z.3
  • 27
    • 33747840389 scopus 로고    scopus 로고
    • Tovchigrechko A, Vakser IA. GRAMM-X public web server for protein-protein docking. Nucleic Acids Res 2006;34(Web Server issue):W310-W314.
    • Tovchigrechko A, Vakser IA. GRAMM-X public web server for protein-protein docking. Nucleic Acids Res 2006;34(Web Server issue):W310-W314.
  • 30
    • 12944249776 scopus 로고
    • A discussion of the solution for the best rotation to relate two sets of vectors
    • Kabsch W. A discussion of the solution for the best rotation to relate two sets of vectors. Acta Crystallogr A 1978;34:827-828.
    • (1978) Acta Crystallogr A , vol.34 , pp. 827-828
    • Kabsch, W.1
  • 31
    • 10344232638 scopus 로고    scopus 로고
    • Scoring function for automated assessment of protein structure template quality
    • Zhang Y, Skolnick J. Scoring function for automated assessment of protein structure template quality. Proteins 2004;57:702-710.
    • (2004) Proteins , vol.57 , pp. 702-710
    • Zhang, Y.1    Skolnick, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.