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Volumn 47, Issue 1, 2007, Pages 85-91

Novel, customizable scoring functions, parameterized using N-PLS, for structure-based drug discovery

Author keywords

[No Author keywords available]

Indexed keywords

CRYSTAL STRUCTURE; MOLECULAR STRUCTURE; PARAMETER ESTIMATION; PROTEINS;

EID: 33846889763     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci600357t     Document Type: Article
Times cited : (23)

References (37)
  • 1
    • 33846867352 scopus 로고    scopus 로고
    • National Institute of General Medical Sciences, Protein Structure Initiative NIGMS-PSI, accessed Sep 29, 2006
    • National Institute of General Medical Sciences - Protein Structure Initiative (NIGMS-PSI). http://www.nigms.nih.gov/Initiatives/PSI (accessed Sep 29, 2006).
  • 2
    • 33749260698 scopus 로고    scopus 로고
    • Warren, G. L.; Andrews, W. C.; Capelli, A. M.; Clarke, B.; LaLonde, J.; Lambert, M. H.; Lindvall, M.; Nevins, N.; Semus, S. F; Senger, S.; Tedesco, G.; Wall, I. D.; Woolven, J. M.; Peishoff, C. E.; Head, M. S. A Critical Assessment of Docking Programs and Scoring Functions. J. Med. Chem. 2006, 49, 5912-5931.
    • Warren, G. L.; Andrews, W. C.; Capelli, A. M.; Clarke, B.; LaLonde, J.; Lambert, M. H.; Lindvall, M.; Nevins, N.; Semus, S. F; Senger, S.; Tedesco, G.; Wall, I. D.; Woolven, J. M.; Peishoff, C. E.; Head, M. S. A Critical Assessment of Docking Programs and Scoring Functions. J. Med. Chem. 2006, 49, 5912-5931.
  • 3
    • 0029623184 scopus 로고
    • Computational Methods to Predict Binding Free Energy in Ligand-Receptor Complexes
    • Murcko, M. A; Mark, A. Computational Methods to Predict Binding Free Energy in Ligand-Receptor Complexes, J. Med. Chem. 1995, 38, 4953-4967.
    • (1995) J. Med. Chem , vol.38 , pp. 4953-4967
    • Murcko, M.A.1    Mark, A.2
  • 4
    • 0032993815 scopus 로고    scopus 로고
    • Scoring Functions: A View from the Bench
    • Tame, J. R. H. Scoring Functions: A View from the Bench. J. Comput.-Aided Mol. Des. 1999, 13, 99-108.
    • (1999) J. Comput.-Aided Mol. Des , vol.13 , pp. 99-108
    • Tame, J.R.H.1
  • 5
    • 0032112137 scopus 로고    scopus 로고
    • Prediction of Binding Constants of Protein Ligands: A Fast Method for the Prioritization 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 Prioritization 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
  • 6
    • 11644261806 scopus 로고    scopus 로고
    • Automated Docking Using a Lamarckian Genetic Algorithm and an Empirical Binding Free Energy Function
    • (a) Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; 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    Olson, A.J.6
  • 7
    • 33846858726 scopus 로고    scopus 로고
    • Autodock, version 2.04, accessed Sep 29, 2006
    • (b) Autodock, version 2.04. http://www.scripps.edu/mb/olson/doc/ autodock (accessed Sep 29, 2006).
  • 8
    • 0031552362 scopus 로고    scopus 로고
    • Development and Validation of a Genetic Algorithm for Flexible Docking
    • Jones G.; Willet, 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    Willet, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
  • 9
    • 85135598119 scopus 로고    scopus 로고
    • 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.
    • 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.
  • 10
    • 0033545622 scopus 로고    scopus 로고
    • A General and Fast Scoring Function for Protein-Ligand Interactions: A Simplified Interaction Approach
    • Muegge, I.; Martin, Y. C. A General and Fast Scoring Function for Protein-Ligand Interactions: A Simplified Interaction Approach. J. Med. Chem. 1999, 42, 791-804.
    • (1999) J. Med. Chem , vol.42 , pp. 791-804
    • Muegge, I.1    Martin, Y.C.2
  • 11
    • 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
  • 12
    • 33846864077 scopus 로고    scopus 로고
    • Cerius2, version 4.6; Accelrys: San Diego, CA, accessed Sep 29, 2006
    • Cerius2, version 4.6; Accelrys: San Diego, CA. http://www.accelrys.com/products/cerius2/cerius2products/listing.html (accessed Sep 29, 2006).
  • 13
    • 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
  • 14
    • 0030599010 scopus 로고    scopus 로고
    • 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.
    • 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.
  • 15
    • 0031226772 scopus 로고    scopus 로고
    • Empirical Scoring Functions: 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: 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
  • 16
    • 0032533791 scopus 로고    scopus 로고
    • Flexible Docking Using Tabu Search and an Empirical Estimate of Binding Affinity
    • Baxter, C. A.; Murray, C. W.; Clark, D. E.; Westhead, D. R.; Eldridge, M. D. Flexible Docking Using Tabu Search and an Empirical Estimate of Binding Affinity. Proteins 1998, 33, 367-382.
    • (1998) Proteins , vol.33 , pp. 367-382
    • Baxter, C.A.1    Murray, C.W.2    Clark, D.E.3    Westhead, D.R.4    Eldridge, M.D.5
  • 17
    • 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, 11-26.
    • (2002) J. Comput.-Aided Mol. Des , vol.16 , pp. 11-26
    • Wang, R.1    Lai, L.2    Wang, S.3
  • 18
    • 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
  • 19
    • 0037763817 scopus 로고    scopus 로고
    • Wang, S. Comparative Evaluation of 11 Scoring Functions for Molecular Docking
    • Wang, R.; Lu, Yipin; Wang, S. Comparative Evaluation of 11 Scoring Functions for Molecular Docking. J. Med. Chem. 2003, 46, 2287-2303.
    • (2003) J. Med. Chem , vol.46 , pp. 2287-2303
    • Wang, R.1    Lu, Y.2
  • 20
    • 0035312864 scopus 로고    scopus 로고
    • Statistical Potentials and Scoring Functions Applied to Protein-Ligand Binding
    • Gohlke, H.; Klebe, G. Statistical Potentials and Scoring Functions Applied to Protein-Ligand Binding. Curr. Opin. Struct. Biol. 2001, 11, 231-235.
    • (2001) Curr. Opin. Struct. Biol , vol.11 , pp. 231-235
    • Gohlke, H.1    Klebe, G.2
  • 21
    • 0031181346 scopus 로고    scopus 로고
    • Powerful, Rapid Computer Algorithms for Structure-Based Design
    • (a) McMartin, C.; Bohacek, R. S. QXP: Powerful, Rapid Computer Algorithms for Structure-Based Design. J. Comput.-Aided Mol. Des. 1997, 11, 333-344.
    • (1997) J. Comput.-Aided Mol. Des , vol.11 , pp. 333-344
    • McMartin, C.1    Bohacek, R.S.Q.2
  • 22
    • 33846886438 scopus 로고    scopus 로고
    • QXP_Flo+, version August 2002: Thistlesoft: Colebrook, CT.
    • (b) QXP_Flo+, version August 2002: Thistlesoft: Colebrook, CT.
  • 23
    • 33846868942 scopus 로고    scopus 로고
    • Research Collaboratory for Structural Bioinformatics, Protein Data Bank, accessed Sep 29, 2006
    • Research Collaboratory for Structural Bioinformatics - Protein Data Bank. http://www.rcsb.org/pdb/ (accessed Sep 29, 2006).
  • 24
    • 33846853839 scopus 로고    scopus 로고
    • PLS-Toolbox for Use with MATLAB. version 3.0: Eigenvector Research: Manson, WA, 2003
    • PLS-Toolbox for Use with MATLAB. version 3.0: Eigenvector Research: Manson, WA, 2003.
  • 25
    • 84875208117 scopus 로고    scopus 로고
    • Schrödinger: Portland, OR, accessed Sep 29
    • MacroModel; Schrödinger: Portland, OR. http://www. schrodinger.com/ProductDescription.php?mID=6&sID=8 (accessed Sep 29, 2006).
    • (2006) MacroModel
  • 26
    • 0003009442 scopus 로고    scopus 로고
    • Multiway Calibration - Multilinear PLS
    • Bro, R. Multiway Calibration - Multilinear PLS. J. Chemom. 1996, 10, 47-61.
    • (1996) J. Chemom , vol.10 , pp. 47-61
    • Bro, R.1
  • 27
    • 0035965040 scopus 로고    scopus 로고
    • On the Difference between Low Rank and Subspace Approximation: Improved Model for Multi-Linear PLS Regression
    • Bro, R.; Smilde, A. K.; de Jong, S. On the Difference between Low Rank and Subspace Approximation: Improved Model for Multi-Linear PLS Regression. Chemom. Intell. Lab. Syst. 2001, 58, 3-13.
    • (2001) Chemom. Intell. Lab. Syst , vol.58 , pp. 3-13
    • Bro, R.1    Smilde, A.K.2    de Jong, S.3
  • 28
    • 0032112137 scopus 로고    scopus 로고
    • Prediction of Binding Constants of Protein Ligands: A Fast Method for the Prioritization 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 Prioritization 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
  • 29
    • 0029995624 scopus 로고    scopus 로고
    • Head, R. D.; Smythe, M. L; Oprea, T. I.; Waller, C. L.; Green, S. M.: Marshall, G. R. VALIDATE: A New Method for the Receptor-Based Prediction of Binding Affinities of Novel Ligands. J. Am. Chem. Soc. 1996, 118, 3959-3969.
    • Head, R. D.; Smythe, M. L; Oprea, T. I.; Waller, C. L.; Green, S. M.: Marshall, G. R. VALIDATE: A New Method for the Receptor-Based Prediction of Binding Affinities of Novel Ligands. J. Am. Chem. Soc. 1996, 118, 3959-3969.
  • 30
    • 0031226772 scopus 로고    scopus 로고
    • Empirical Scoring Functions: 1. 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: 1. 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
  • 31
    • 0038205821 scopus 로고    scopus 로고
    • Analysis and Optimization of Structure-Based Virtual Screening Protocols. (3). New Methods and Old Problems in Scoring Function Design
    • Smith, R.; Hubbard, R. E.; Gschwend, D. A.; Leach, A. R.; Good, A. C. Analysis and Optimization of Structure-Based Virtual Screening Protocols. (3). New Methods and Old Problems in Scoring Function Design. J. Mol. Graphics Modell. 2003, 22, 41-53.
    • (2003) J. Mol. Graphics Modell , vol.22 , pp. 41-53
    • Smith, R.1    Hubbard, R.E.2    Gschwend, D.A.3    Leach, A.R.4    Good, A.C.5
  • 32
    • 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
  • 33
    • 15244346501 scopus 로고    scopus 로고
    • Krammer, A.; Kirchhoff, P. D.; Jiang, X.; Venkatachalam, C. M.; Waldman, M. LigScore: A Novel Scoring Function for Predicting Binding Affinities. J. Mol. Graphics Modell. 2005, 23, 395-407.
    • Krammer, A.; Kirchhoff, P. D.; Jiang, X.; Venkatachalam, C. M.; Waldman, M. LigScore: A Novel Scoring Function for Predicting Binding Affinities. J. Mol. Graphics Modell. 2005, 23, 395-407.
  • 34
    • 33846862329 scopus 로고    scopus 로고
    • McMartin, C. QXP_Flo+ 200 Complex Training Set. Personal communication.
    • McMartin, C. QXP_Flo+ 200 Complex Training Set. Personal communication.
  • 36
    • 27144489164 scopus 로고    scopus 로고
    • Burges, C. J. C. A Tutorial on Support Vector Machines for Pattern Recognition. Data Min. Knowledge Discovery 1998, 2, 121-167.
    • Burges, C. J. C. A Tutorial on Support Vector Machines for Pattern Recognition. Data Min. Knowledge Discovery 1998, 2, 121-167.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.