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Volumn 83, Issue 5, 2015, Pages 891-897

Protein models docking benchmark 2

Author keywords

Modeling of protein complexes; Protein interactions; Protein modeling; Protein recognition; Structure prediction

Indexed keywords

ACCURACY; ARTICLE; MOLECULAR DOCKING; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN STRUCTURE; QUALITY CONTROL; RELIABILITY; STRUCTURE ANALYSIS; AMINO ACID SEQUENCE; CHEMISTRY; MOLECULAR GENETICS; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN SECONDARY STRUCTURE; STANDARD; STANDARDS;

EID: 84927695321     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24784     Document Type: Article
Times cited : (21)

References (27)
  • 1
    • 67650497792 scopus 로고    scopus 로고
    • Nature of the protein universe
    • Levitt M. Nature of the protein universe. Proc Natl Acad Sci USA 2009;106:11079-11084.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 11079-11084
    • Levitt, M.1
  • 2
    • 84883479032 scopus 로고    scopus 로고
    • Protein modeling: what happened to the "protein structure gap"?
    • Schwede T. Protein modeling: what happened to the "protein structure gap"?. Structure 2013;21:1531-1540.
    • (2013) Structure , vol.21 , pp. 1531-1540
    • Schwede, T.1
  • 3
    • 84908263546 scopus 로고    scopus 로고
    • Protein-protein docking: from interaction to interactome
    • Vakser IA. Protein-protein docking: from interaction to interactome. Biophys J 2014;107:1785-1793.
    • (2014) Biophys J , vol.107 , pp. 1785-1793
    • Vakser, I.A.1
  • 4
    • 84878552481 scopus 로고    scopus 로고
    • Low-resolution structural modeling of protein interactome
    • Vakser IA. Low-resolution structural modeling of protein interactome. Curr Opin Struct Biol 2013;23:198-205.
    • (2013) Curr Opin Struct Biol , vol.23 , pp. 198-205
    • Vakser, I.A.1
  • 5
    • 13844255392 scopus 로고    scopus 로고
    • Protein complexes: structure prediction challenges for the 21st century
    • Aloy P, Pichaud M, Russell RB. Protein complexes: structure prediction challenges for the 21st century. Curr Opin Struct Biol 2005;15:15-22.
    • (2005) Curr Opin Struct Biol , vol.15 , pp. 15-22
    • Aloy, P.1    Pichaud, M.2    Russell, R.B.3
  • 6
    • 84890029384 scopus 로고    scopus 로고
    • Template-based structure modeling of protein-protein interactions
    • Szilagyi A, Zhang Y. Template-based structure modeling of protein-protein interactions. Curr Opin Struct Biol 2014;24:10-23.
    • (2014) Curr Opin Struct Biol , vol.24 , pp. 10-23
    • Szilagyi, A.1    Zhang, Y.2
  • 7
    • 84862625522 scopus 로고    scopus 로고
    • Constructing structural networks of signaling pathways on the proteome scale
    • Kuzu G, Keskin O, Gursoy A, Nussinov R. Constructing structural networks of signaling pathways on the proteome scale. Curr Opin Struct Biol 2012;22:367-377.
    • (2012) Curr Opin Struct Biol , vol.22 , pp. 367-377
    • Kuzu, G.1    Keskin, O.2    Gursoy, A.3    Nussinov, R.4
  • 8
    • 84878282902 scopus 로고    scopus 로고
    • Toward a "structural BLAST": using structural relationships to infer function
    • Dey F, Zhang QC, Petrey D, Honig B. Toward a "structural BLAST": using structural relationships to infer function. Protein Sci 2013;22:359-366.
    • (2013) Protein Sci , vol.22 , pp. 359-366
    • Dey, F.1    Zhang, Q.C.2    Petrey, D.3    Honig, B.4
  • 9
    • 36749060694 scopus 로고    scopus 로고
    • DOCKGROUND system of databases for protein recognition studies: unbound structures for docking
    • Gao Y, Douguet D, Tovchigrechko A, Vakser IA. DOCKGROUND system of databases for protein recognition studies: unbound structures for docking. Proteins 2007;69:845-851.
    • (2007) Proteins , vol.69 , pp. 845-851
    • Gao, Y.1    Douguet, D.2    Tovchigrechko, A.3    Vakser, I.A.4
  • 10
    • 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
  • 13
    • 0000603016 scopus 로고
    • A method for determining reaction paths in large molecules-application to myoglobin
    • Elber R, Karplus M. A method for determining reaction paths in large molecules-application to myoglobin. Chem Phys Lett 1987;139:375-380.
    • (1987) Chem Phys Lett , vol.139 , pp. 375-380
    • Elber, R.1    Karplus, M.2
  • 14
    • 0942268404 scopus 로고    scopus 로고
    • A super-linear minimization scheme for the nudged elastic band method
    • Chu JW, Trout BL, Brooks BR. A super-linear minimization scheme for the nudged elastic band method. J Chem Phys 2003;119:12708-12717.
    • (2003) J Chem Phys , vol.119 , pp. 12708-12717
    • Chu, J.W.1    Trout, B.L.2    Brooks, B.R.3
  • 15
    • 77954065271 scopus 로고    scopus 로고
    • ITASSER: a unified platform for automated protein structure and function prediction
    • Roy A, Kucukural A, Zhang Y. ITASSER: a unified platform for automated protein structure and function prediction. Nat Protocols 2010;5:725-738.
    • (2010) Nat Protocols , vol.5 , pp. 725-738
    • Roy, A.1    Kucukural, A.2    Zhang, Y.3
  • 16
    • 39449115394 scopus 로고    scopus 로고
    • ITASSER server for protein 3D structure prediction
    • Zhang Y. ITASSER server for protein 3D structure prediction. BMC Bioinform 2008;9:40.
    • (2008) BMC Bioinform , vol.9 , pp. 40
    • Zhang, Y.1
  • 18
    • 0009130599 scopus 로고    scopus 로고
    • A structural explanation for the twilight zone of protein sequence homology
    • Chung SY, Subbiah S. A structural explanation for the twilight zone of protein sequence homology. Structure 1996;4:1123-1127.
    • (1996) Structure , vol.4 , pp. 1123-1127
    • Chung, S.Y.1    Subbiah, S.2
  • 19
    • 81255123286 scopus 로고    scopus 로고
    • Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization
    • Xu D, Zhang Y. Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. Biophys J 2011;101:2525-2534.
    • (2011) Biophys J , vol.101 , pp. 2525-2534
    • Xu, D.1    Zhang, Y.2
  • 20
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 22
    • 84893482610 scopus 로고
    • A solution for the best rotation to relate two sets of vectors
    • Kabsch W. A solution for the best rotation to relate two sets of vectors. Acta Cryst A 1976;32:922-923.
    • (1976) Acta Cryst A , vol.32 , pp. 922-923
    • Kabsch, W.1
  • 23
    • 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 Cryst A 1978;34:827-828.
    • (1978) Acta Cryst A , vol.34 , pp. 827-828
    • Kabsch, W.1
  • 24
    • 0042622381 scopus 로고    scopus 로고
    • LGA: a method for finding 3D similarities in protein structures
    • Zemla A. LGA: a method for finding 3D similarities in protein structures. Nucl Acid Res 2003;31:3370-3374.
    • (2003) Nucl Acid Res , vol.31 , pp. 3370-3374
    • Zemla, A.1
  • 25
    • 80054685109 scopus 로고    scopus 로고
    • Critical assessment of methods of protein structure prediction (CASP)-round IX
    • Moult J, Fidelis K, Kryshtafovych A, Tramontano A. Critical assessment of methods of protein structure prediction (CASP)-round IX. Proteins 2011;79:1-5.
    • (2011) Proteins , vol.79 , pp. 1-5
    • Moult, J.1    Fidelis, K.2    Kryshtafovych, A.3    Tramontano, A.4
  • 26
    • 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
  • 27
    • 84888289172 scopus 로고    scopus 로고
    • Docking, scoring, and affinity prediction in CAPRI
    • Lensink MF, Wodak SJ. Docking, scoring, and affinity prediction in CAPRI. Proteins 2013;81:2082-2095.
    • (2013) Proteins , vol.81 , pp. 2082-2095
    • Lensink, M.F.1    Wodak, S.J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.