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Volumn 6, Issue 4, 2011, Pages

A collaborative filtering approach for protein-protein docking scoring functions

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; CLASSIFIER; CONTROLLED STUDY; DECISION TREE; GENETIC ALGORITHM; MOLECULAR DOCKING; PROCESS DEVELOPMENT; PROCESS OPTIMIZATION; PROTEIN CONFORMATION; PROTEIN FUNCTION; PROTEIN PROTEIN DOCKING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SCORING SYSTEM; SUPPORT VECTOR MACHINE; VALIDATION PROCESS; ALGORITHM; AREA UNDER THE CURVE; CHEMISTRY; METABOLISM; METHODOLOGY; PROTEIN ANALYSIS; PROTEIN DATABASE;

EID: 79955536838     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0018541     Document Type: Article
Times cited : (25)

References (28)
  • 1
    • 0036424666 scopus 로고    scopus 로고
    • Structural basis of macromolecular recognition
    • Wodak SJ, Janin J, (2002) Structural basis of macromolecular recognition. Adv Protein Chem 61: 9-73.
    • (2002) Adv Protein Chem , vol.61 , pp. 9-73
    • Wodak, S.J.1    Janin, J.2
  • 2
    • 63849310190 scopus 로고    scopus 로고
    • The cartographers toolbox: building bigger and better human protein interaction networks
    • Sanderson CM, (2009) The cartographers toolbox: building bigger and better human protein interaction networks. Brief Funct Genomic Proteomic 8: 1-11.
    • (2009) Brief Funct Genomic Proteomic , vol.8 , pp. 1-11
    • Sanderson, C.M.1
  • 4
    • 41949111630 scopus 로고    scopus 로고
    • Recent progress and future directions in protein-protein docking
    • Ritchie DW, (2008) Recent progress and future directions in protein-protein docking. Curr Protein Pept Sci 9: 1-15.
    • (2008) Curr Protein Pept Sci , vol.9 , pp. 1-15
    • Ritchie, D.W.1
  • 5
    • 70049112107 scopus 로고    scopus 로고
    • Pushing structural information into the yeast interactome by high-throughput protein docking experiments
    • Mosca R, Pons C, Fernández-Recio J, Aloy P, (2009) Pushing structural information into the yeast interactome by high-throughput protein docking experiments. PLoS Comput Biol 5: e1000490.
    • (2009) PLoS Comput Biol , vol.5 , pp. 1000490
    • Mosca, R.1    Pons, C.2    Fernández-Recio, J.3    Aloy, P.4
  • 6
    • 77952068704 scopus 로고    scopus 로고
    • Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark
    • Kastritis PL, Bonvin AM, (2010) Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark. J Proteome Res 9: 2216-25.
    • (2010) J Proteome Res , vol.9 , pp. 2216-2225
    • Kastritis, P.L.1    Bonvin, A.M.2
  • 7
    • 0036606483 scopus 로고    scopus 로고
    • Principles of docking: An overview of search algorithms and a guide to scoring functions
    • Halperin I, Ma B, Wolfson H, Nussinov R, (2002) Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins 47: 409-43.
    • (2002) Proteins , vol.47 , pp. 409-443
    • Halperin, I.1    Ma, B.2    Wolfson, H.3    Nussinov, R.4
  • 9
    • 40049091293 scopus 로고    scopus 로고
    • DiMoVo: a Voronoi tessellationbased method for discriminating crystallographic and biological protein-protein interactions
    • Bernauer J, Bahadur RP, Rodier F, Janin J, Poupon A, (2008) DiMoVo: a Voronoi tessellationbased method for discriminating crystallographic and biological protein-protein interactions. Bioinformatics 24: 652-8.
    • (2008) Bioinformatics , vol.24 , pp. 652-658
    • Bernauer, J.1    Bahadur, R.P.2    Rodier, F.3    Janin, J.4    Poupon, A.5
  • 10
    • 21644458290 scopus 로고    scopus 로고
    • A docking analysis of the statistical physics of protein-protein recognition
    • Bernauer J, Poupon A, Azé J, Janin J, (2005) A docking analysis of the statistical physics of protein-protein recognition. Phys Biol 2: S17-23.
    • (2005) Phys Biol , vol.2 , pp. 17-23
    • Bernauer, J.1    Poupon, A.2    Azé, J.3    Janin, J.4
  • 11
    • 34047129815 scopus 로고    scopus 로고
    • A new protein-protein docking scoring function based on interface residue properties
    • Bernauer J, Azé J, Janin J, Poupon A, (2007) A new protein-protein docking scoring function based on interface residue properties. Bioinformatics 23: 555-62.
    • (2007) Bioinformatics , vol.23 , pp. 555-562
    • Bernauer, J.1    Azé, J.2    Janin, J.3    Poupon, A.4
  • 14
    • 0030598343 scopus 로고    scopus 로고
    • Deviations from standard atomic volumes as a quality measure for protein crystal structures
    • Pontius J, Richelle J, Wodak S, (1996) Deviations from standard atomic volumes as a quality measure for protein crystal structures. J Mol Biol 264: 121-36.
    • (1996) J Mol Biol , vol.264 , pp. 121-136
    • Pontius, J.1    Richelle, J.2    Wodak, S.3
  • 16
    • 0028961335 scopus 로고
    • SCOP: a structural classification of proteins database for the investigation of sequences and structures
    • Murzin A, Brenner S, Hubbard T, Chothia C, (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247: 536-40.
    • (1995) J Mol Biol , vol.247 , pp. 536-540
    • Murzin, A.1    Brenner, S.2    Hubbard, T.3    Chothia, C.4
  • 19
    • 0347082050 scopus 로고    scopus 로고
    • Making large-scale support vector machine learning practical
    • Cambridge, MA, USA, MIT Press
    • Joachims T, (1999) Making large-scale support vector machine learning practical. Cambridge, MA, USA MIT Press pp. 169-184.
    • (1999) , pp. 169-184
    • Joachims, T.1
  • 20
    • 0038359614 scopus 로고    scopus 로고
    • CAPRI: a Critical Assessment of PRedicted Interactions
    • Janin J, Henrick K, Moult J, Eyck L, Sternberg M, et al. (2003) CAPRI: a Critical Assessment of PRedicted Interactions. Proteins 52: 2-9.
    • (2003) Proteins , vol.52 , pp. 2-9
    • Janin, J.1    Henrick, K.2    Moult, J.3    Eyck, L.4    Sternberg, M.5
  • 21
    • 36749006579 scopus 로고    scopus 로고
    • Docking and scoring protein complexes: CAPRI 3rd Edition
    • Lensink MF, Mendez R, Wodak SJ, (2007) Docking and scoring protein complexes: CAPRI 3rd Edition. Proteins 69: 704-18.
    • (2007) Proteins , vol.69 , pp. 704-718
    • Lensink, M.F.1    Mendez, R.2    Wodak, S.J.3
  • 22
    • 37549021146 scopus 로고    scopus 로고
    • Binding of Rac1, Rnd1, and RhoD to a novel Rho GTPase interaction motif destabilizes dimerization of the plexin-B1 effector domain
    • Tong Y, Chugha P, Hota PK, Alviani RS, Li M, et al. (2007) Binding of Rac1, Rnd1, and RhoD to a novel Rho GTPase interaction motif destabilizes dimerization of the plexin-B1 effector domain. J Biol Chem 282: 37215-24.
    • (2007) J Biol Chem , vol.282 , pp. 37215-37224
    • Tong, Y.1    Chugha, P.2    Hota, P.K.3    Alviani, R.S.4    Li, M.5
  • 23
    • 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, (2005) Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins 60: 150-69.
    • (2005) Proteins , vol.60 , pp. 150-169
    • Mendez, R.1    Leplae, R.2    Lensink, M.F.3    Wodak, S.J.4
  • 25
    • 0003798627 scopus 로고    scopus 로고
    • Advances in kernel methods - support vector learning
    • Schölkopf B, Burges CJ, (1998) Advances in kernel methods- support vector learning.
    • (1998)
    • Schölkopf, B.1    Burges, C.J.2
  • 26
    • 0003500248 scopus 로고
    • C4.5: Programs for Machine Learning
    • Morgan Kaufmann
    • Quinlan JR, (1993) C4.5: Programs for Machine Learning. Morgan Kaufmann.
    • (1993)
    • Quinlan, J.R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.