메뉴 건너뛰기




Volumn 46, Issue 12, 2003, Pages 2287-2303

Comparative evaluation of 11 scoring functions for molecular docking

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BINDING AFFINITY; CHEMSCORE; COMPLEX FORMATION; CONFORMATION; D SCORE; DRUGSCORE; EVALUATION; F SCORE; G SCORE; LIGSCORE; LUDI SCORE; PLP SCORE; PMF SCORE; RATING SCALE; X SCORE;

EID: 0037763817     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm0203783     Document Type: Article
Times cited : (841)

References (30)
  • 1
    • 0035025191 scopus 로고    scopus 로고
    • DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
    • Ewing, T. J. A.; 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.A.1    Makino, S.2    Skillman, A.G.3    Kuntz, I.D.4
  • 2
    • 11644261806 scopus 로고    scopus 로고
    • Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
    • Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem. 1998, 19, 1639-1662.
    • (1998) J. Comput. Chem. , vol.19 , pp. 1639-1662
    • Morris, G.M.1    Goodsell, D.S.2    Halliday, R.S.3    Huey, R.4    Hart, W.E.5    Belew, R.K.6    Olson, A.J.7
  • 3
    • 0030599010 scopus 로고    scopus 로고
    • A fast flexible docking method using an incremental construction algorithm
    • Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol. 1996, 261, 470-489.
    • (1996) J. Mol. Biol. , vol.261 , pp. 470-489
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.4
  • 4
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; Taylor, R. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 1997, 267, 727-748.
    • (1997) J. Mol. Biol. , vol.267 , pp. 727-748
    • Jones, G.1    Willett, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
  • 5
    • 0031226772 scopus 로고    scopus 로고
    • Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
    • Eldridge, M. D.; Murray, C. W.; Auton, T. R.; Paolini, G. V.; Mee, R. P. Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J. Comput.-Aided Mol. Des. 1997, 11, 425-445.
    • (1997) J. Comput.-Aided Mol. Des. , vol.11 , pp. 425-445
    • Eldridge, M.D.1    Murray, C.W.2    Auton, T.R.3    Paolini, G.V.4    Mee, R.P.5
  • 6
    • 0029294584 scopus 로고
    • Molecular recognition of the inhibitor AG-1343 by HIV-1 Protease: Conformationally flexible docking by evolutionary programming
    • Gehlhaar, D. K.; Verkhivker, G. M.; Rejto, P. A.; Sherman, C. J.; Fogel, D. B.; Fogel, L. J.; Freer, S. T. Molecular recognition of the inhibitor AG-1343 by HIV-1 Protease: Conformationally flexible docking by evolutionary programming. Chem. Biol. 1995, 2, 317-324.
    • (1995) Chem. Biol. , vol.2 , pp. 317-324
    • Gehlhaar, D.K.1    Verkhivker, G.M.2    Rejto, P.A.3    Sherman, C.J.4    Fogel, D.B.5    Fogel, L.J.6    Freer, S.T.7
  • 8
    • 0028454828 scopus 로고
    • The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
    • Böhm, H. J. The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J. Comput.-Aided Mol. Des. 1994, 8, 243-256.
    • (1994) J. Comput.-Aided Mol. Des. , vol.8 , pp. 243-256
    • Böhm, H.J.1
  • 9
    • 0032112137 scopus 로고    scopus 로고
    • Prediction of binding constants of protein ligands: A fast method for the polarization of hits obtained from de novo design or 3D database search programs
    • Böhm, H. J. Prediction of binding constants of protein ligands: a fast method for the polarization of hits obtained from de novo design or 3D database search programs. J. Comput.-Aided Mol. Des. 1998, 12, 309-323.
    • (1998) J. Comput.-Aided Mol. Des. , vol.12 , pp. 309-323
    • Böhm, H.J.1
  • 10
    • 0001704085 scopus 로고    scopus 로고
    • SCORE A new empirical method for estimating the binding affinity of a protein-ligand complex
    • Wang, R.; Gao, Y.; Lai, L. SCORE: A new empirical method for estimating the binding affinity of a protein-ligand complex. J. Mol. Model. 1998, 4, 379-394.
    • (1998) J. Mol. Model , vol.4 , pp. 379-394
    • Wang, R.1    Gao, Y.2    Lai, L.3
  • 11
    • 0036022960 scopus 로고    scopus 로고
    • Further development and validation of empirical scoring functions for structure-based binding affinity prediction
    • Wang, R.; Lai, L.; Wang, S. Further development and validation of empirical scoring functions for structure-based binding affinity prediction. J. Comput.-Aided Mol. Des. 2002, 16(2), 11-26.
    • (2002) J. Comput.-Aided Mol. Des. , vol.16 , Issue.2 , pp. 11-26
    • Wang, R.1    Lai, L.2    Wang, S.3
  • 12
    • 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
  • 13
    • 0033673508 scopus 로고    scopus 로고
    • A knowledge-based scoring function for protein-ligand interactions: Probing the reference state
    • Muegge, I. A knowledge-based scoring function for protein-ligand interactions: Probing the reference state. Perspect. Drug Discovery Des. 2000, 20, 99-114.
    • (2000) Perspect. Drug Discovery Des. , vol.20 , pp. 99-114
    • Muegge, I.1
  • 14
    • 0001745748 scopus 로고    scopus 로고
    • Effect of ligand volume correction on PMF scoring
    • Muegge, I. Effect of ligand volume correction on PMF scoring. J. Comput. Chem. 2001, 22, 418-425.
    • (2001) J. Comput. Chem. , vol.22 , pp. 418-425
    • Muegge, I.1
  • 15
    • 0034645763 scopus 로고    scopus 로고
    • Knowledge-based scoring function to predict protein-ligand interactions
    • Gohlke, H.; Hendlich, M.; Klebe, G. Knowledge-based scoring function to predict protein-ligand interactions. J. Mol. Biol. 2000, 295, 337-356.
    • (2000) J. Mol. Biol. , vol.295 , pp. 337-356
    • Gohlke, H.1    Hendlich, M.2    Klebe, G.3
  • 16
    • 0037142298 scopus 로고    scopus 로고
    • Small molecule growth 2001 (SMoG2001): An improved knowledge-based scoring function for protein-ligand interactions
    • Ishchenko, A. V.; Shakhnovich, E. I. Small molecule growth 2001 (SMoG2001): An improved knowledge-based scoring function for protein-ligand interactions. J. Med. Chem. 2002, 45, 2770-2780.
    • (2002) J. Med. Chem. , vol.45 , pp. 2770-2780
    • Ishchenko, A.V.1    Shakhnovich, E.I.2
  • 17
    • 0034649618 scopus 로고    scopus 로고
    • Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations
    • Bissantz, C.; Folkers, G.; Rognan, D. Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. J. Med. Chem. 2000, 43, 4759-4767.
    • (2000) J. Med. Chem. , vol.43 , pp. 4759-4767
    • Bissantz, C.1    Folkers, G.2    Rognan, D.3
  • 18
    • 0035966871 scopus 로고    scopus 로고
    • Detailed analysis of scoring functions for virtual screening
    • Stahl, M.; Rarey, M. Detailed analysis of scoring functions for virtual screening. J. Med. Chem. 2001, 44, 1035-1042.
    • (2001) J. Med. Chem. , vol.44 , pp. 1035-1042
    • Stahl, M.1    Rarey, M.2
  • 19
    • 0035811458 scopus 로고    scopus 로고
    • A new concept for multidimensional selection of ligand conformations (multiselect) and multidimensional scoring (multiscore) of protein-ligand binding affinities
    • Terp, G. E.; Johansen, B. N.; Christensen, I. T.; Jorgensen, F. S. A new concept for multidimensional selection of ligand conformations (MultiSelect) and multidimensional scoring (MultiScore) of protein-ligand binding affinities. J. Med. Chem. 2001, 44, 2333-2343.
    • (2001) J. Med. Chem. , vol.44 , pp. 2333-2343
    • Terp, G.E.1    Johansen, B.N.2    Christensen, I.T.3    Jorgensen, F.S.4
  • 20
    • 0036606204 scopus 로고    scopus 로고
    • ConsDock: A new program for the consensus analysis of protein-ligand interactions
    • Paul, N.; Rognan, D. ConsDock: A new program for the consensus analysis of protein-ligand interactions. Proteins: Struct., Funct., Genet. 2002, 47, 521-533.
    • (2002) Proteins: Struct., Funct., Genet. , vol.47 , pp. 521-533
    • Paul, N.1    Rognan, D.2
  • 24
    • 0033576680 scopus 로고    scopus 로고
    • Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins
    • Charifson, P. S.; Corkery, J. J.; Murcko, M. A.; Walters, W. P. Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins. J. Med. Chem. 1999, 42, 5100-5109.
    • (1999) J. Med. Chem. , vol.42 , pp. 5100-5109
    • Charifson, P.S.1    Corkery, J.J.2    Murcko, M.A.3    Walters, W.P.4
  • 26
    • 0035438402 scopus 로고    scopus 로고
    • How does consensus scoring work for virtual library screening? An idealized computer experiment
    • Wang, R.; Wang, S. How does consensus scoring work for virtual library screening? An idealized computer experiment. J. Chem. Inf. Comput. Sci. 2001, 41, 1422-1426.
    • (2001) J. Chem. Inf. Comput. Sci. , vol.41 , pp. 1422-1426
    • Wang, R.1    Wang, S.2
  • 28
    • 0036535895 scopus 로고    scopus 로고
    • Protein folding: The free energy surface
    • and the references therein
    • Gruebele, M. Protein folding: The free energy surface. Curr. Opin. Struct. Biol. 2002, 12, 161-168 and the references therein.
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 161-168
    • Gruebele, M.1
  • 29
    • 0032961895 scopus 로고    scopus 로고
    • The particle concept: Placing discrete water molecules during protein-ligand docking predictions
    • Rarey, M.; Kramer, B.; Lengauer, T. The particle concept: placing discrete water molecules during protein-ligand docking predictions. Proteins: Struct., Funct., Genet. 1999, 4, 17-28.
    • (1999) Proteins: Struct., Funct., Genet. , vol.4 , pp. 17-28
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3
  • 30
    • 0021757436 scopus 로고
    • A new force field for molecular mechanical simulation of nucleic acids and proteins
    • Weiner, S. J.; Kollman, P. A.; Case, D. A. A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 1984, 106, 765-784.
    • (1984) J. Am. Chem. Soc. , vol.106 , pp. 765-784
    • Weiner, S.J.1    Kollman, P.A.2    Case, D.A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.