메뉴 건너뛰기




Volumn 53, Issue 8, 2013, Pages 1905-1914

Automated large-scale file preparation, docking, and scoring: Evaluation of ITScore and STScore using the 2012 community structure-activity resource benchmark

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; CRYSTALS; FORECASTING; IMPORTANCE SAMPLING; KNOWLEDGE BASED SYSTEMS; LIGANDS; PROTEINS;

EID: 84883240307     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci400045v     Document Type: Article
Times cited : (19)

References (24)
  • 2
    • 34249040810 scopus 로고    scopus 로고
    • Physics-based methods for studying protein-ligand interactions
    • Huang, N.; Jacobson, M. P. Physics-based methods for studying protein-ligand interactions Curr. Opin. Drug Discovery Dev. 2007, 30, 325-331
    • (2007) Curr. Opin. Drug Discovery Dev. , vol.30 , pp. 325-331
    • Huang, N.1    Jacobson, M.P.2
  • 3
    • 77957898063 scopus 로고    scopus 로고
    • Scoring functions and their evaluation methods for protein-ligand docking: Recent advances and future directions
    • Huang, S.-Y.; Grinter, S. Z.; Zou, X. Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions Phys. Chem. Chem. Phys. 2010, 12, 12899-12908
    • (2010) Phys. Chem. Chem. Phys. , vol.12 , pp. 12899-12908
    • Huang, S.-Y.1    Grinter, S.Z.2    Zou, X.3
  • 4
    • 77957899529 scopus 로고    scopus 로고
    • Advances and challenges in protein-ligand docking
    • Huang, S.-Y.; Zou, X. Advances and challenges in protein-ligand docking Phys. Chem. Chem. Phys. 2010, 11, 3016-3034
    • (2010) Phys. Chem. Chem. Phys. , vol.11 , pp. 3016-3034
    • Huang, S.-Y.1    Zou, X.2
  • 7
    • 33750555073 scopus 로고    scopus 로고
    • An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials
    • Huang, S.-Y.; Zou, X. An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials J. Comput. Chem. 2006, 27, 1866-1875
    • (2006) J. Comput. Chem. , vol.27 , pp. 1866-1875
    • Huang, S.-Y.1    Zou, X.2
  • 8
    • 33750574927 scopus 로고    scopus 로고
    • An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function
    • Huang, S.-Y.; Zou, X. An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function J. Comput. Chem. 2006, 27, 1876-1882
    • (2006) J. Comput. Chem. , vol.27 , pp. 1876-1882
    • Huang, S.-Y.1    Zou, X.2
  • 9
    • 0029976427 scopus 로고    scopus 로고
    • Statistical Potentials Extracted from Protein Structures: How Accurate Are They?
    • Thomas, P. D.; Dill, K. A. Statistical Potentials Extracted From Protein Structures: How Accurate Are They? J. Mol. Biol. 1996, 257, 457-469
    • (1996) J. Mol. Biol. , vol.257 , pp. 457-469
    • Thomas, P.D.1    Dill, K.A.2
  • 10
    • 77955800755 scopus 로고    scopus 로고
    • Mean-force scoring functions for protein-ligand binding
    • Huang, S.-Y.; Zou, X. Mean-force scoring functions for protein-ligand binding Annu. Rep. Comput. Chem. 2010, 6, 281-296
    • (2010) Annu. Rep. Comput. Chem. , vol.6 , pp. 281-296
    • Huang, S.-Y.1    Zou, X.2
  • 11
    • 0033545622 scopus 로고    scopus 로고
    • A general and fast scoring function for protein-ligand interactions: A simplified potential approach
    • Muegge, I.; Martin, Y.-C. A general and fast scoring function for protein-ligand interactions: a simplified potential approach J. Med. Chem. 1999, 42, 791-804
    • (1999) J. Med. Chem. , vol.42 , pp. 791-804
    • Muegge, I.1    Martin, Y.-C.2
  • 12
    • 0000823044 scopus 로고    scopus 로고
    • BLEEP - A Potential of mean force describing protein-ligand interactions: I. Generating potential
    • Mitchell, J. B. O.; Laskowski, R. A.; Alex, A.; Thornton, J. M. BLEEP-A Potential of mean force describing protein-ligand interactions: I. Generating potential J. Comput. Chem. 1999, 20, 1165-1176
    • (1999) J. Comput. Chem. , vol.20 , pp. 1165-1176
    • Mitchell, J.B.O.1    Laskowski, R.A.2    Alex, A.3    Thornton, J.M.4
  • 13
    • 17144383951 scopus 로고    scopus 로고
    • A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes
    • Zhang, C.; Liu, S.; Zhu, Q.; Zhou, Y. A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes J. Med. Chem. 2005, 48, 2325-2335
    • (2005) J. Med. Chem. , vol.48 , pp. 2325-2335
    • Zhang, C.1    Liu, S.2    Zhu, Q.3    Zhou, Y.4
  • 14
    • 26444588137 scopus 로고    scopus 로고
    • DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction
    • Velec, H. F.; Gohlke, H.; Klebe, G. DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction J. Med. Chem. 2005, 48, 6296-6303
    • (2005) J. Med. Chem. , vol.48 , pp. 6296-6303
    • Velec, H.F.1    Gohlke, H.2    Klebe, G.3
  • 15
    • 84986432941 scopus 로고
    • Automated docking with grid-based energy approach to macromolecule-ligand interactions
    • Meng, E. C.; Shoichet, B. K.; Kuntz, I. D. Automated docking with grid-based energy approach to macromolecule-ligand interactions J. Comput. Chem. 1992, 13, 505-524
    • (1992) J. Comput. Chem. , vol.13 , pp. 505-524
    • Meng, E.C.1    Shoichet, B.K.2    Kuntz, I.D.3
  • 16
    • 0035025191 scopus 로고    scopus 로고
    • DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
    • Ewing, T. J.; Makino, S.; Skillman, A. G.; Kuntz, I. D. DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases J. Comput. Aided Mol. Des. 2001, 15, 411-428
    • (2001) J. Comput. Aided Mol. Des. , vol.15 , pp. 411-428
    • Ewing, T.J.1    Makino, S.2    Skillman, A.G.3    Kuntz, I.D.4
  • 18
    • 0023965741 scopus 로고
    • SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules
    • Weininger, D. SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules J. Chem. Inf. Comput. Sci. 1988, 28, 31-36
    • (1988) J. Chem. Inf. Comput. Sci. , vol.28 , pp. 31-36
    • Weininger, D.1
  • 19
    • 33846000313 scopus 로고    scopus 로고
    • Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking
    • Huang, S.-Y.; Zou, X. Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking Proteins: Struct., Funct., Bioinf. 2007, 66, 399-421
    • (2007) Proteins: Struct., Funct., Bioinf. , vol.66 , pp. 399-421
    • Huang, S.-Y.1    Zou, X.2
  • 20
    • 33845923184 scopus 로고    scopus 로고
    • Efficient molecular docking of NMR structures: Application to HIV-1 protease
    • Huang, S.-Y.; Zou, X. Efficient molecular docking of NMR structures: application to HIV-1 protease Protein Sci. 2007, 16, 43-51
    • (2007) Protein Sci. , vol.16 , pp. 43-51
    • Huang, S.-Y.1    Zou, X.2
  • 22
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte, J.; Doolittle, R. F. A simple method for displaying the hydropathic character of a protein J. Mol. Biol. 1982, 157, 105-132
    • (1982) J. Mol. Biol. , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 23
    • 80053297657 scopus 로고    scopus 로고
    • Scoring and lessons learned with the CSAR benchmark using an improved iterative knowledge-based scoring function
    • Huang, S.-Y.; Zou, X. Scoring and lessons learned with the CSAR benchmark using an improved iterative knowledge-based scoring function J. Chem. Inf. Model. 2011, 51, 2097-2106
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 2097-2106
    • Huang, S.-Y.1    Zou, X.2
  • 24
    • 80053322295 scopus 로고    scopus 로고
    • Construction and test of ligand decoy sets using MDock: Community Structure-Activity Resource benchmarks for binding mode prediction
    • Huang, S.-Y.; Zou, X. Construction and test of ligand decoy sets using MDock: Community Structure-Activity Resource benchmarks for binding mode prediction J. Chem. Inf. Model. 2011, 51, 2107-2114
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 2107-2114
    • Huang, S.-Y.1    Zou, X.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.