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Volumn 51, Issue 12, 2011, Pages 3078-3092

Statistical potential for modeling and ranking of protein-ligand interactions

Author keywords

[No Author keywords available]

Indexed keywords

ATOMS; BINDING SITES; COMPLEXATION; CRYSTAL ATOMIC STRUCTURE; GEOMETRY; LEARNING TO RANK; MEAN SQUARE ERROR; MOLECULES; PROBABILITY; PROTEINS; WELL TESTING;

EID: 84555220606     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci200377u     Document Type: Article
Times cited : (58)

References (128)
  • 2
    • 33749245117 scopus 로고    scopus 로고
    • Prediction of protein-ligand interactions. Docking and scoring: Successes and gaps
    • Leach, A. R.; Shoichet, B. K.; Peishoff, C. E. Prediction of protein-ligand interactions. Docking and scoring: Successes and gaps J. Med. Chem. 2006, 49 (20) 5851-5855
    • (2006) J. Med. Chem. , vol.49 , Issue.20 , pp. 5851-5855
    • Leach, A.R.1    Shoichet, B.K.2    Peishoff, C.E.3
  • 3
    • 33745199815 scopus 로고    scopus 로고
    • Virtual ligand screening: Strategies, perspectives and limitations
    • Klebe, G. Virtual ligand screening: strategies, perspectives and limitations Drug Discovery Today 2006, 11 (13-14) 580-594
    • (2006) Drug Discovery Today , vol.11 , Issue.13-14 , pp. 580-594
    • Klebe, G.1
  • 5
    • 33749513370 scopus 로고    scopus 로고
    • Scoring functions for protein-ligand docking
    • Jain, A. N. Scoring functions for protein-ligand docking Curr. Protein Pept. Sci. 2006, 7 (5) 407-420
    • (2006) Curr. Protein Pept. Sci. , vol.7 , Issue.5 , pp. 407-420
    • Jain, A.N.1
  • 6
    • 53249117061 scopus 로고    scopus 로고
    • Evaluation of ligand-binding affinity using polynomial empirical scoring functions
    • de Azevedo, W. F.; Dias, R. Evaluation of ligand-binding affinity using polynomial empirical scoring functions Bioorg. Med. Chem. 2008, 16 (20) 9378-9382
    • (2008) Bioorg. Med. Chem. , vol.16 , Issue.20 , pp. 9378-9382
    • De Azevedo, W.F.1    Dias, R.2
  • 7
    • 41949126416 scopus 로고    scopus 로고
    • Molecular recognition and binding free energy calculations in drug development
    • Dominy, B. N. Molecular recognition and binding free energy calculations in drug development Curr. Pharm. Biotechnol. 2008, 9 (2) 87-95
    • (2008) Curr. Pharm. Biotechnol. , vol.9 , Issue.2 , pp. 87-95
    • Dominy, B.N.1
  • 8
    • 33746465842 scopus 로고    scopus 로고
    • Dock around the clock - Current status of small molecule docking and scoring
    • Rester, U. Dock around the clock-Current status of small molecule docking and scoring QSAR Comb. Sci. 2006, 25 (7) 605-615
    • (2006) QSAR Comb. Sci. , vol.25 , Issue.7 , pp. 605-615
    • Rester, U.1
  • 9
    • 33749449880 scopus 로고    scopus 로고
    • Docking and scoring - Theoretically easy, practically impossible?
    • Coupez, B.; Lewis, R. A. Docking and scoring-Theoretically easy, practically impossible? Curr. Med. Chem. 2006, 13 (25) 2995-3003
    • (2006) Curr. Med. Chem. , vol.13 , Issue.25 , pp. 2995-3003
    • Coupez, B.1    Lewis, R.A.2
  • 10
    • 1942471391 scopus 로고    scopus 로고
    • Assessing scoring functions for protein-ligand interactions
    • Ferrara, P.; Gohlke, H.; Price, D. J.; Klebe, G.; Brooks, C. L. Assessing scoring functions for protein-ligand interactions J. Med. Chem. 2004, 47 (12) 3032-3047
    • (2004) J. Med. Chem. , vol.47 , Issue.12 , pp. 3032-3047
    • Ferrara, P.1    Gohlke, H.2    Price, D.J.3    Klebe, G.4    Brooks, C.L.5
  • 11
    • 0037763817 scopus 로고    scopus 로고
    • Comparative evaluation of 11 scoring functions for molecular docking
    • Wang, R. X.; Lu, Y. P.; Wang, S. M. Comparative evaluation of 11 scoring functions for molecular docking J. Med. Chem. 2003, 46 (12) 2287-2303
    • (2003) J. Med. Chem. , vol.46 , Issue.12 , pp. 2287-2303
    • Wang, R.X.1    Lu, Y.P.2    Wang, S.M.3
  • 12
    • 0037008160 scopus 로고    scopus 로고
    • Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors
    • Gohlke, H.; Klebe, G. Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors Angew. Chem., Int. Ed. 2002, 41 (15) 2645-2676
    • (2002) Angew. Chem., Int. Ed. , vol.41 , Issue.15 , pp. 2645-2676
    • Gohlke, H.1    Klebe, G.2
  • 15
    • 0029912748 scopus 로고    scopus 로고
    • Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
    • Jorgensen, W. L.; Maxwell, D. S.; TiradoRives, J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids J. Am. Chem. Soc. 1996, 118 (45) 11225-11236
    • (1996) J. Am. Chem. Soc. , vol.118 , Issue.45 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tiradorives, J.3
  • 16
    • 0001751804 scopus 로고    scopus 로고
    • Parametrization of aliphatic CHn united atoms of GROMOS96 force field
    • Daura, X.; Mark, A. E.; van Gunsteren, W. F. Parametrization of aliphatic CHn united atoms of GROMOS96 force field J. Comput. Chem. 1998, 19 (5) 535-547
    • (1998) J. Comput. Chem. , vol.19 , Issue.5 , pp. 535-547
    • Daura, X.1    Mark, A.E.2    Van Gunsteren, W.F.3
  • 18
    • 5244268272 scopus 로고    scopus 로고
    • Merck molecular force field. 5. Extension of MMFF94 using experimental data, additional computational data, and empirical rules
    • Halgren, T. A. Merck molecular force field. 5. Extension of MMFF94 using experimental data, additional computational data, and empirical rules J. Comput. Chem. 1996, 17 (5-6) 616-641
    • (1996) J. Comput. Chem. , vol.17 , Issue.5-6 , pp. 616-641
    • Halgren, T.A.1
  • 19
    • 84986432941 scopus 로고
    • Automated Docking with Grid-Based Energy Evaluation
    • Meng, E. C.; Shoichet, B. K.; Kuntz, I. D. Automated Docking with Grid-Based Energy Evaluation J. Comput. Chem. 1992, 13 (4) 505-524
    • (1992) J. Comput. Chem. , vol.13 , Issue.4 , pp. 505-524
    • Meng, E.C.1    Shoichet, B.K.2    Kuntz, I.D.3
  • 20
    • 0033536456 scopus 로고    scopus 로고
    • Inclusion of solvation in ligand binding free energy calculations using the generalized-born model
    • Zou, X. Q.; Sun, Y. X.; Kuntz, I. D. Inclusion of solvation in ligand binding free energy calculations using the generalized-born model J. Am. Chem. Soc. 1999, 121 (35) 8033-8043
    • (1999) J. Am. Chem. Soc. , vol.121 , Issue.35 , pp. 8033-8043
    • Zou, X.Q.1    Sun, Y.X.2    Kuntz, I.D.3
  • 21
    • 5244324671 scopus 로고    scopus 로고
    • Molecular mechanics (MM4) calculations on conjugated hydrocarbons
    • Nevins, N.; Lii, J. H.; Allinger, N. L. Molecular mechanics (MM4) calculations on conjugated hydrocarbons J. Comput. Chem. 1996, 17 (5-6) 695-729
    • (1996) J. Comput. Chem. , vol.17 , Issue.5-6 , pp. 695-729
    • Nevins, N.1    Lii, J.H.2    Allinger, N.L.3
  • 22
    • 84988115618 scopus 로고
    • Validation of the General-Purpose Tripos 5.2 Force-Field
    • Clark, M.; Cramer, R. D.; Vanopdenbosch, N. Validation of the General-Purpose Tripos 5.2 Force-Field J. Comput. Chem. 1989, 10 (8) 982-1012
    • (1989) J. Comput. Chem. , vol.10 , Issue.8 , pp. 982-1012
    • Clark, M.1    Cramer, R.D.2    Vanopdenbosch, N.3
  • 23
    • 4444282928 scopus 로고    scopus 로고
    • A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6
    • Oostenbrink, C.; Villa, A.; Mark, A. E.; Van Gunsteren, W. F. A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6 J. Comput. Chem. 2004, 25 (13) 1656-1676
    • (2004) J. Comput. Chem. , vol.25 , Issue.13 , pp. 1656-1676
    • Oostenbrink, C.1    Villa, A.2    Mark, A.E.3    Van Gunsteren, W.F.4
  • 25
    • 77957222180 scopus 로고    scopus 로고
    • Rapid Context-Dependent Ligand Desolvation in Molecular Docking
    • Mysinger, M. M.; Shoichet, B. K. Rapid Context-Dependent Ligand Desolvation in Molecular Docking J. Chem. Inf. Model. 2010, 50 (9) 1561-1573
    • (2010) J. Chem. Inf. Model. , vol.50 , Issue.9 , pp. 1561-1573
    • Mysinger, M.M.1    Shoichet, B.K.2
  • 26
    • 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 (14) 1639-1662
    • (1998) J. Comput. Chem. , vol.19 , Issue.14 , 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
  • 27
    • 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 (5) 791-804
    • (1999) J. Med. Chem. , vol.42 , Issue.5 , pp. 791-804
    • Muegge, I.1    Martin, Y.C.2
  • 28
    • 0000882405 scopus 로고    scopus 로고
    • BLEEP - Potential of mean force describing protein-ligand interactions: II. Calculation of binding energies and comparison with experimental data
    • Mitchell, J. B. O.; Laskowski, R. A.; Alex, A.; Forster, M. J.; Thornton, J. M. BLEEP-Potential of mean force describing protein-ligand interactions: II. Calculation of binding energies and comparison with experimental data J. Comput. Chem. 1999, 20 (11) 1177-1185
    • (1999) J. Comput. Chem. , vol.20 , Issue.11 , pp. 1177-1185
    • Mitchell, J.B.O.1    Laskowski, R.A.2    Alex, A.3    Forster, M.J.4    Thornton, J.M.5
  • 29
    • 0000823044 scopus 로고    scopus 로고
    • BLEEP - Potential of mean force describing protein-ligand interactions: I. Generating potential
    • Mitchell, J. B. O.; Laskowski, R. A.; Alex, A.; Thornton, J. M. BLEEP-Potential of mean force describing protein-ligand interactions: I. Generating potential J. Comput. Chem. 1999, 20 (11) 1165-1176
    • (1999) J. Comput. Chem. , vol.20 , Issue.11 , pp. 1165-1176
    • Mitchell, J.B.O.1    Laskowski, R.A.2    Alex, A.3    Thornton, J.M.4
  • 30
    • 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 (2) 337-356
    • (2000) J. Mol. Biol. , vol.295 , Issue.2 , pp. 337-356
    • Gohlke, H.1    Hendlich, M.2    Klebe, G.3
  • 31
    • 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 (5) 317-324
    • (1995) Chem. Biol. , vol.2 , Issue.5 , 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
  • 32
    • 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 (7) 1035-1042
    • (2001) J. Med. Chem. , vol.44 , Issue.7 , pp. 1035-1042
    • Stahl, M.1    Rarey, M.2
  • 33
    • 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 (13) 2770-2780
    • (2002) J. Med. Chem. , vol.45 , Issue.13 , pp. 2770-2780
    • Ishchenko, A.V.1    Shakhnovich, E.I.2
  • 34
    • 16644380565 scopus 로고    scopus 로고
    • PLASS: Protein-ligand affinity statistical score - A knowledge-based force-field model of interaction derived from the PDB
    • Ozrin, V. D.; Subbotin, M. V.; Nikitin, S. M. PLASS: Protein-ligand affinity statistical score-a knowledge-based force-field model of interaction derived from the PDB J. Comput.-Aided Mol. Des. 2004, 18 (4) 261-270
    • (2004) J. Comput.-Aided Mol. Des. , vol.18 , Issue.4 , pp. 261-270
    • Ozrin, V.D.1    Subbotin, M.V.2    Nikitin, S.M.3
  • 35
    • 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. G.; 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 (20) 6296-6303
    • (2005) J. Med. Chem. , vol.48 , Issue.20 , pp. 6296-6303
    • Velec, H.F.G.1    Gohlke, H.2    Klebe, G.3
  • 36
    • 20544447896 scopus 로고    scopus 로고
    • Knowledge based potentials: The reverse Boltzmann methodology, virtual screening and molecular weight dependence
    • Kirtay, C. K.; Mitchell, J. B. O.; Lumley, J. A. Knowledge based potentials: the reverse Boltzmann methodology, virtual screening and molecular weight dependence QSAR Comb. Sci. 2005, 24 (4) 527-536
    • (2005) QSAR Comb. Sci. , vol.24 , Issue.4 , pp. 527-536
    • Kirtay, C.K.1    Mitchell, J.B.O.2    Lumley, J.A.3
  • 37
    • 33846889763 scopus 로고    scopus 로고
    • Novel, customizable scoring functions, parameterized using N-PLS, for structure-based drug discovery
    • Catana, C.; Stouten, P. F. W. Novel, customizable scoring functions, parameterized using N-PLS, for structure-based drug discovery J. Chem. Inf. Model. 2007, 47 (1) 85-91
    • (2007) J. Chem. Inf. Model. , vol.47 , Issue.1 , pp. 85-91
    • Catana, C.1    Stouten, P.F.W.2
  • 38
    • 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. Q. An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials J. Comput. Chem. 2006, 27 (15) 1866-1875
    • (2006) J. Comput. Chem. , vol.27 , Issue.15 , pp. 1866-1875
    • Huang, S.Y.1    Zou, X.Q.2
  • 39
    • 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. Q. An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function J. Comput. Chem. 2006, 27 (15) 1876-1882
    • (2006) J. Comput. Chem. , vol.27 , Issue.15 , pp. 1876-1882
    • Huang, S.Y.1    Zou, X.Q.2
  • 40
    • 77649221514 scopus 로고    scopus 로고
    • Inclusion of Solvation and Entropy in the Knowledge-Based Scoring Function for Protein-Ligand Interactions
    • Huang, S. Y.; Zou, X. Q. Inclusion of Solvation and Entropy in the Knowledge-Based Scoring Function for Protein-Ligand Interactions J. Chem. Inf. Model. 2010, 50 (2) 262-273
    • (2010) J. Chem. Inf. Model. , vol.50 , Issue.2 , pp. 262-273
    • Huang, S.Y.1    Zou, X.Q.2
  • 41
    • 0032153192 scopus 로고    scopus 로고
    • Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the model
    • Murray, C. W.; Auton, T. R.; Eldridge, M. D. Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the model J. Comput.-Aided Mol. Des. 1998, 12 (5) 503-519
    • (1998) J. Comput.-Aided Mol. Des. , vol.12 , Issue.5 , pp. 503-519
    • Murray, C.W.1    Auton, T.R.2    Eldridge, M.D.3
  • 42
    • 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 (5) 425-445
    • (1997) J. Comput.-Aided Mol. Des. , vol.11 , Issue.5 , pp. 425-445
    • Eldridge, M.D.1    Murray, C.W.2    Auton, T.R.3    Paolini, G.V.4    Mee, R.P.5
  • 43
    • 11644261806 scopus 로고    scopus 로고
    • Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
    • Olson, A. J.; Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function J. Comput. Chem. 1998, 19 (14) 1639-1662
    • (1998) J. Comput. Chem. , vol.19 , Issue.14 , pp. 1639-1662
    • Olson, A.J.1    Morris, G.M.2    Goodsell, D.S.3    Halliday, R.S.4    Huey, R.5    Hart, W.E.6    Belew, R.K.7
  • 44
    • 0036022960 scopus 로고    scopus 로고
    • Further development and validation of empirical scoring functions for structure-based binding affinity prediction
    • Wang, S. M.; Wang, R. X.; Lai, L. H. Further development and validation of empirical scoring functions for structure-based binding affinity prediction J. Comput.-Aided Mol. Des. 2002, 16 (1) 11-26
    • (2002) J. Comput.-Aided Mol. Des. , vol.16 , Issue.1 , pp. 11-26
    • Wang, S.M.1    Wang, R.X.2    Lai, L.H.3
  • 45
    • 0842332235 scopus 로고    scopus 로고
    • A practical approach to docking of zinc metalloproteinase inhibitors
    • Hu, X.; Balaz, S.; Shelver, W. H. A practical approach to docking of zinc metalloproteinase inhibitors J. Mol. Graphics Modell. 2004, 22 (4) 293-307
    • (2004) J. Mol. Graphics Modell. , vol.22 , Issue.4 , pp. 293-307
    • Hu, X.1    Balaz, S.2    Shelver, W.H.3
  • 47
    • 26944499806 scopus 로고    scopus 로고
    • POEM: Parameter optimization using ensemble methods: Application to target specific scoring functions
    • Antes, I.; Merkwirth, C.; Lengauer, T. POEM: Parameter optimization using ensemble methods: Application to target specific scoring functions J. Chem. Inf. Model. 2005, 45 (5) 1291-1302
    • (2005) J. Chem. Inf. Model. , vol.45 , Issue.5 , pp. 1291-1302
    • Antes, I.1    Merkwirth, C.2    Lengauer, T.3
  • 48
    • 27444445346 scopus 로고    scopus 로고
    • PostDOCK: A structural, empirical approach to scoring protein ligand complexes
    • Springer, C.; Adalsteinsson, H.; Young, M. M.; Kegelmeyer, P. W.; Roe, D. C. PostDOCK: A structural, empirical approach to scoring protein ligand complexes J. Med. Chem. 2005, 48 (22) 6821-6831
    • (2005) J. Med. Chem. , vol.48 , Issue.22 , pp. 6821-6831
    • Springer, C.1    Adalsteinsson, H.2    Young, M.M.3    Kegelmeyer, P.W.4    Roe, D.C.5
  • 49
    • 33745369874 scopus 로고    scopus 로고
    • Hierarchical PLS modeling for predicting the binding of a comprehensive set of structurally diverse protein-ligand complexes
    • Linusson, A.; Lindstrom, A.; Pettersson, F.; Almqvist, F.; Berglund, A.; Kihlberg, J. Hierarchical PLS modeling for predicting the binding of a comprehensive set of structurally diverse protein-ligand complexes J. Chem. Inf. Model. 2006, 46 (3) 1154-1167
    • (2006) J. Chem. Inf. Model. , vol.46 , Issue.3 , pp. 1154-1167
    • Linusson, A.1    Lindstrom, A.2    Pettersson, F.3    Almqvist, F.4    Berglund, A.5    Kihlberg, J.6
  • 52
    • 0001752768 scopus 로고    scopus 로고
    • The Cambridge Structural Database: A quarter of a million crystal structures and rising
    • Allen, F. H. The Cambridge Structural Database: a quarter of a million crystal structures and rising Acta Crystallogr., Sect. B: Struct. Sci. 2002, 58, 380-388
    • (2002) Acta Crystallogr., Sect. B: Struct. Sci. , vol.58 , pp. 380-388
    • Allen, F.H.1
  • 53
    • 0025008445 scopus 로고
    • Identification of Native Protein Folds Amongst a Large Number of Incorrect Models - The Calculation of Low-Energy Conformations from Potentials of Mean Force
    • Hendlich, M.; Lackner, P.; Weitckus, S.; Floeckner, H.; Froschauer, R.; Gottsbacher, K.; Casari, G.; Sippl, M. J. Identification of Native Protein Folds Amongst a Large Number of Incorrect Models-the Calculation of Low-Energy Conformations from Potentials of Mean Force J. Mol. Biol. 1990, 216 (1) 167-180
    • (1990) J. Mol. Biol. , vol.216 , Issue.1 , pp. 167-180
    • Hendlich, M.1    Lackner, P.2    Weitckus, S.3    Floeckner, H.4    Froschauer, R.5    Gottsbacher, K.6    Casari, G.7    Sippl, M.J.8
  • 54
    • 0027180507 scopus 로고
    • Verification of Protein Structures - Patterns of Nonbonded Atomic Interactions
    • Colovos, C.; Yeates, T. O. Verification of Protein Structures-Patterns of Nonbonded Atomic Interactions Protein Sci. 1993, 2 (9) 1511-1519
    • (1993) Protein Sci. , vol.2 , Issue.9 , pp. 1511-1519
    • Colovos, C.1    Yeates, T.O.2
  • 55
    • 0027650879 scopus 로고
    • Boltzmann Principle, Knowledge-Based Mean Fields and Protein-Folding - An Approach to the Computational Determination of Protein Structures
    • Sippl, M. J. Boltzmann Principle, Knowledge-Based Mean Fields and Protein-Folding-an Approach to the Computational Determination of Protein Structures J. Comput.-Aided Mol. Des. 1993, 7 (4) 473-501
    • (1993) J. Comput.-Aided Mol. Des. , vol.7 , Issue.4 , pp. 473-501
    • Sippl, M.J.1
  • 56
    • 0032080720 scopus 로고    scopus 로고
    • Influence of protein structure databases on the predictive power of statistical pair potentials
    • Furuichi, E.; Koehl, P. Influence of protein structure databases on the predictive power of statistical pair potentials Proteins: Struct., Funct., Bioinf. 1998, 31 (2) 139-149
    • (1998) Proteins: Struct., Funct., Bioinf. , vol.31 , Issue.2 , pp. 139-149
    • Furuichi, E.1    Koehl, P.2
  • 57
    • 0028318094 scopus 로고
    • Factors Influencing the Ability of Knowledge-Based Potentials to Identify Native Sequence-Structure Matches
    • Kocher, J. P. A.; Rooman, M. J.; Wodak, S. J. Factors Influencing the Ability of Knowledge-Based Potentials to Identify Native Sequence-Structure Matches J. Mol. Biol. 1994, 235 (5) 1598-1613
    • (1994) J. Mol. Biol. , vol.235 , Issue.5 , pp. 1598-1613
    • Kocher, J.P.A.1    Rooman, M.J.2    Wodak, S.J.3
  • 58
    • 0029101826 scopus 로고
    • Recognizing Native Folds by the Arrangement of Hydrophobic and Polar Residues
    • Huang, E. S.; Subbiah, S.; Levitt, M. Recognizing Native Folds by the Arrangement of Hydrophobic and Polar Residues J. Mol. Biol. 1995, 252 (5) 709-720
    • (1995) J. Mol. Biol. , vol.252 , Issue.5 , pp. 709-720
    • Huang, E.S.1    Subbiah, S.2    Levitt, M.3
  • 59
    • 0029563695 scopus 로고
    • Are database-derived potentials valid for scoring both forward and inverted protein folding?
    • Rooman, M. J.; Wodak, S. J. Are database-derived potentials valid for scoring both forward and inverted protein folding? Protein Eng. 1995, 8 (9) 849-858
    • (1995) Protein Eng. , vol.8 , Issue.9 , pp. 849-858
    • Rooman, M.J.1    Wodak, S.J.2
  • 60
    • 0029942661 scopus 로고    scopus 로고
    • Structure-derived potentials and protein simulations
    • Jernigan, R. L.; Bahar, I. Structure-derived potentials and protein simulations Curr. Opin. Struct. Biol. 1996, 6 (2) 195-209
    • (1996) Curr. Opin. Struct. Biol. , vol.6 , Issue.2 , pp. 195-209
    • Jernigan, R.L.1    Bahar, I.2
  • 61
    • 0029964055 scopus 로고    scopus 로고
    • Potential energy functions for threading
    • Jones, D. T.; Thornton, J. M. Potential energy functions for threading Curr. Opin. Struct. Biol. 1996, 6 (2) 210-216
    • (1996) Curr. Opin. Struct. Biol. , vol.6 , Issue.2 , pp. 210-216
    • Jones, D.T.1    Thornton, J.M.2
  • 62
    • 0029919190 scopus 로고    scopus 로고
    • Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
    • Miyazawa, S.; Jernigan, R. L. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading J. Mol. Biol. 1996, 256 (3) 623-644
    • (1996) J. Mol. Biol. , vol.256 , Issue.3 , pp. 623-644
    • Miyazawa, S.1    Jernigan, R.L.2
  • 63
    • 0030914617 scopus 로고    scopus 로고
    • Comparison of database potentials and molecular mechanics force fields
    • Moult, J. Comparison of database potentials and molecular mechanics force fields Curr. Opin. Struct. Biol. 1997, 7 (2) 194-199
    • (1997) Curr. Opin. Struct. Biol. , vol.7 , Issue.2 , pp. 194-199
    • Moult, J.1
  • 64
    • 0029987862 scopus 로고    scopus 로고
    • Energy functions that discriminate X-ray and near native folds from well-constructed decoys
    • Park, B.; Levitt, M. Energy functions that discriminate X-ray and near native folds from well-constructed decoys J. Mol. Biol. 1996, 258 (2) 367-92
    • (1996) J. Mol. Biol. , vol.258 , Issue.2 , pp. 367-392
    • Park, B.1    Levitt, M.2
  • 65
    • 0031557390 scopus 로고    scopus 로고
    • Factors affecting the ability of energy functions to discriminate correct from incorrect folds
    • Park, B. H.; Huang, E. S.; Levitt, M. Factors affecting the ability of energy functions to discriminate correct from incorrect folds J. Mol. Biol. 1997, 266 (4) 831-46
    • (1997) J. Mol. Biol. , vol.266 , Issue.4 , pp. 831-846
    • Park, B.H.1    Huang, E.S.2    Levitt, M.3
  • 66
    • 0030781040 scopus 로고    scopus 로고
    • Residue-residue mean-force potentials for protein structure recognition
    • Reva, B. A.; Finkelstein, A. V.; Sanner, M. F.; Olson, A. J. Residue-residue mean-force potentials for protein structure recognition Protein Eng. 1997, 10 (8) 865-876
    • (1997) Protein Eng. , vol.10 , Issue.8 , pp. 865-876
    • Reva, B.A.1    Finkelstein, A.V.2    Sanner, M.F.3    Olson, A.J.4
  • 67
    • 0031585984 scopus 로고    scopus 로고
    • Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
    • Simons, K. T.; Kooperberg, C.; Huang, E.; Baker, D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions J. Mol. Biol. 1997, 268 (1) 209-25
    • (1997) J. Mol. Biol. , vol.268 , Issue.1 , pp. 209-225
    • Simons, K.T.1    Kooperberg, C.2    Huang, E.3    Baker, D.4
  • 68
    • 0030968991 scopus 로고    scopus 로고
    • Empirical potentials and functions for protein folding and binding
    • Vajda, S.; Sippl, M.; Novotny, J. Empirical potentials and functions for protein folding and binding Curr. Opin. Struct. Biol. 1997, 7 (2) 222-228
    • (1997) Curr. Opin. Struct. Biol. , vol.7 , Issue.2 , pp. 222-228
    • Vajda, S.1    Sippl, M.2    Novotny, J.3
  • 69
    • 0030777760 scopus 로고    scopus 로고
    • Predicting protein stability changes upon mutation using database-derived potentials: Solvent accessibility determines the importance of local versus non-local interactions along the sequence
    • Gilis, D.; Rooman, M. Predicting protein stability changes upon mutation using database-derived potentials: Solvent accessibility determines the importance of local versus non-local interactions along the sequence J. Mol. Biol. 1997, 272 (2) 276-290
    • (1997) J. Mol. Biol. , vol.272 , Issue.2 , pp. 276-290
    • Gilis, D.1    Rooman, M.2
  • 70
    • 0032488962 scopus 로고    scopus 로고
    • An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
    • Samudrala, R.; Moult, J. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction J. Mol. Biol. 1998, 275 (5) 895-916
    • (1998) J. Mol. Biol. , vol.275 , Issue.5 , pp. 895-916
    • Samudrala, R.1    Moult, J.2
  • 71
    • 0033005899 scopus 로고    scopus 로고
    • Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes
    • Betancourt, M. R.; Thirumalai, D. Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes Protein Sci. 1999, 8 (2) 361-369
    • (1999) Protein Sci. , vol.8 , Issue.2 , pp. 361-369
    • Betancourt, M.R.1    Thirumalai, D.2
  • 72
    • 0033537993 scopus 로고    scopus 로고
    • GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences
    • Jones, D. T. GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences J. Mol. Biol. 1999, 287 (4) 797-815
    • (1999) J. Mol. Biol. , vol.287 , Issue.4 , pp. 797-815
    • Jones, D.T.1
  • 74
    • 0032929780 scopus 로고    scopus 로고
    • Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins
    • Simons, K. T.; Ruczinski, I.; Kooperberg, C.; Fox, B. A.; Bystroff, C.; Baker, D. Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins Proteins: Struct., Funct., Genet. 1999, 34 (1) 82-95
    • (1999) Proteins: Struct., Funct., Genet. , vol.34 , Issue.1 , pp. 82-95
    • Simons, K.T.1    Ruczinski, I.2    Kooperberg, C.3    Fox, B.A.4    Bystroff, C.5    Baker, D.6
  • 75
    • 0034635955 scopus 로고    scopus 로고
    • A statistical mechanical method to optimize energy functions for protein folding
    • Bastolla, U.; Vendruscolo, M.; Knapp, E. W. A statistical mechanical method to optimize energy functions for protein folding Proc. Natl. Acad. Sci. U. S. A. 2000, 97 (8) 3977-3981
    • (2000) Proc. Natl. Acad. Sci. U. S. A. , vol.97 , Issue.8 , pp. 3977-3981
    • Bastolla, U.1    Vendruscolo, M.2    Knapp, E.W.3
  • 76
    • 0034333083 scopus 로고    scopus 로고
    • How to generate improved potentials for protein tertiary structure prediction: A lattice model study
    • Chiu, T. L.; Goldstein, R. A. How to generate improved potentials for protein tertiary structure prediction: a lattice model study Proteins 2000, 41 (2) 157-63
    • (2000) Proteins , vol.41 , Issue.2 , pp. 157-163
    • Chiu, T.L.1    Goldstein, R.A.2
  • 77
    • 0034560338 scopus 로고    scopus 로고
    • Discrimination of near-native protein structures from misfolded models by empirical free energy functions
    • Gatchell, D. W.; Dennis, S.; Vajda, S. Discrimination of near-native protein structures from misfolded models by empirical free energy functions Proteins: Struct., Funct., Genet. 2000, 41 (4) 518-534
    • (2000) Proteins: Struct., Funct., Genet. , vol.41 , Issue.4 , pp. 518-534
    • Gatchell, D.W.1    Dennis, S.2    Vajda, S.3
  • 78
    • 0034031680 scopus 로고    scopus 로고
    • Effective energy functions for protein structure prediction
    • Lazaridis, T.; Karplus, M. Effective energy functions for protein structure prediction Curr. Opin. Struct. Biol. 2000, 10 (2) 139-145
    • (2000) Curr. Opin. Struct. Biol. , vol.10 , Issue.2 , pp. 139-145
    • Lazaridis, T.1    Karplus, M.2
  • 79
    • 0034141931 scopus 로고    scopus 로고
    • Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading?
    • Vendruscolo, M.; Najmanovich, R.; Domany, E. Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading? Proteins: Struct., Funct., Genet. 2000, 38 (2) 134-148
    • (2000) Proteins: Struct., Funct., Genet. , vol.38 , Issue.2 , pp. 134-148
    • Vendruscolo, M.1    Najmanovich, R.2    Domany, E.3
  • 80
    • 0035882533 scopus 로고    scopus 로고
    • A distance-dependent atomic knowledge-based potential for improved protein structure selection
    • Lu, H.; Skolnick, J. A distance-dependent atomic knowledge-based potential for improved protein structure selection Proteins 2001, 44 (3) 223-32
    • (2001) Proteins , vol.44 , Issue.3 , pp. 223-232
    • Lu, H.1    Skolnick, J.2
  • 81
    • 0036145846 scopus 로고    scopus 로고
    • Statistical potentials for fold assessment
    • Melo, F.; Sanchez, R.; Sali, A. Statistical potentials for fold assessment Protein Sci. 2002, 11 (2) 430-48
    • (2002) Protein Sci. , vol.11 , Issue.2 , pp. 430-448
    • Melo, F.1    Sanchez, R.2    Sali, A.3
  • 82
    • 0038708222 scopus 로고    scopus 로고
    • A novel approach to decoy set generation: Designing a physical energy function having local minima with native structure characteristics
    • Keasar, C.; Levitt, M. A novel approach to decoy set generation: designing a physical energy function having local minima with native structure characteristics J. Mol. Biol. 2003, 329 (1) 159-74
    • (2003) J. Mol. Biol. , vol.329 , Issue.1 , pp. 159-174
    • Keasar, C.1    Levitt, M.2
  • 83
    • 0036838311 scopus 로고    scopus 로고
    • Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
    • Zhou, H.; Zhou, Y. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction Protein Sci. 2002, 11 (11) 2714-26
    • (2002) Protein Sci. , vol.11 , Issue.11 , pp. 2714-2726
    • Zhou, H.1    Zhou, Y.2
  • 84
    • 0041509110 scopus 로고    scopus 로고
    • Erratum: Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
    • Zhou, H.; Zhou, Y. Erratum: Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction Protein Sci. 2003, 12 (9) 2121
    • (2003) Protein Sci. , vol.12 , Issue.9 , pp. 2121
    • Zhou, H.1    Zhou, Y.2
  • 85
    • 4344697167 scopus 로고    scopus 로고
    • Local propensities and statistical potentials of backbone dihedral angles in proteins
    • Betancourt, M. R.; Skolnick, J. Local propensities and statistical potentials of backbone dihedral angles in proteins J. Mol. Biol. 2004, 342 (2) 635-649
    • (2004) J. Mol. Biol. , vol.342 , Issue.2 , pp. 635-649
    • Betancourt, M.R.1    Skolnick, J.2
  • 86
    • 1842861587 scopus 로고    scopus 로고
    • Development of novel statistical potentials for protein fold recognition
    • Buchete, N. V.; Straub, J. E.; Thirumalai, D. Development of novel statistical potentials for protein fold recognition Curr. Opin. Struct. Biol. 2004, 14 (2) 225-232
    • (2004) Curr. Opin. Struct. Biol. , vol.14 , Issue.2 , pp. 225-232
    • Buchete, N.V.1    Straub, J.E.2    Thirumalai, D.3
  • 87
    • 1842454935 scopus 로고    scopus 로고
    • Orientational potentials extracted from protein structures improve native fold recognition
    • Buchete, N. V.; Straub, J. E.; Thirumalai, D. Orientational potentials extracted from protein structures improve native fold recognition Protein Sci. 2004, 13 (4) 862-874
    • (2004) Protein Sci. , vol.13 , Issue.4 , pp. 862-874
    • Buchete, N.V.1    Straub, J.E.2    Thirumalai, D.3
  • 88
    • 4544355522 scopus 로고    scopus 로고
    • Improved protein structure selection using decoy-dependent discriminatory functions
    • Wang, K.; Fain, B.; Levitt, M.; Samudrala, R. Improved protein structure selection using decoy-dependent discriminatory functions BMC Struct. Biol. 2004, 4 (1) 8
    • (2004) BMC Struct. Biol. , vol.4 , Issue.1 , pp. 8
    • Wang, K.1    Fain, B.2    Levitt, M.3    Samudrala, R.4
  • 89
    • 2942694535 scopus 로고    scopus 로고
    • The dependence of all-atom statistical potentials on structural training database
    • Zhang, C.; Liu, S.; Zhou, H.; Zhou, Y. The dependence of all-atom statistical potentials on structural training database Biophys. J. 2004, 86 (6) 3349-58
    • (2004) Biophys. J. , vol.86 , Issue.6 , pp. 3349-3358
    • Zhang, C.1    Liu, S.2    Zhou, H.3    Zhou, Y.4
  • 90
    • 22244483130 scopus 로고    scopus 로고
    • Lessons from the design of a novel atomic potential for protein folding
    • Chen, W. W.; Shakhnovich, E. I. Lessons from the design of a novel atomic potential for protein folding Protein Sci. 2005, 14 (7) 1741-1752
    • (2005) Protein Sci. , vol.14 , Issue.7 , pp. 1741-1752
    • Chen, W.W.1    Shakhnovich, E.I.2
  • 91
    • 19544371352 scopus 로고    scopus 로고
    • A consistent set of statistical potentials for quantifying local side-chain and backbone interactions
    • Fang, Q. J.; Shortle, D. A consistent set of statistical potentials for quantifying local side-chain and backbone interactions Proteins: Struct., Funct., Bioinf. 2005, 60 (1) 90-96
    • (2005) Proteins: Struct., Funct., Bioinf. , vol.60 , Issue.1 , pp. 90-96
    • Fang, Q.J.1    Shortle, D.2
  • 92
    • 24344479166 scopus 로고    scopus 로고
    • Atomically detailed potentials to recognize native and approximate protein structures
    • Qiu, J.; Elber, R. Atomically detailed potentials to recognize native and approximate protein structures Proteins: Struct., Funct., Bioinf. 2005, 61 (1) 44-55
    • (2005) Proteins: Struct., Funct., Bioinf. , vol.61 , Issue.1 , pp. 44-55
    • Qiu, J.1    Elber, R.2
  • 93
    • 24644464131 scopus 로고    scopus 로고
    • An atomic environment potential for use in protein structure prediction
    • Summa, C. M.; Levitt, M.; DeGrado, W. F. An atomic environment potential for use in protein structure prediction J. Mol. Biol. 2005, 352 (4) 986-1001
    • (2005) J. Mol. Biol. , vol.352 , Issue.4 , pp. 986-1001
    • Summa, C.M.1    Levitt, M.2    Degrado, W.F.3
  • 94
    • 33744906496 scopus 로고    scopus 로고
    • A new generation of statistical potentials for proteins
    • Dehouck, Y.; Gilis, D.; Rooman, M. A new generation of statistical potentials for proteins Biophys. J. 2006, 90 (11) 4010-4017
    • (2006) Biophys. J. , vol.90 , Issue.11 , pp. 4010-4017
    • Dehouck, Y.1    Gilis, D.2    Rooman, M.3
  • 96
    • 38049051121 scopus 로고    scopus 로고
    • OPUS-PSP: An orientation-dependent statistical all-atom potential derived from side-chain packing
    • Lu, M. Y.; Dousis, A. D.; Ma, J. P. OPUS-PSP: An orientation-dependent statistical all-atom potential derived from side-chain packing J. Mol. Biol. 2008, 376 (1) 288-301
    • (2008) J. Mol. Biol. , vol.376 , Issue.1 , pp. 288-301
    • Lu, M.Y.1    Dousis, A.D.2    Ma, J.P.3
  • 97
    • 34250829219 scopus 로고    scopus 로고
    • OPUS-Ca: A knowledge-based potential function requiring only C alpha positions
    • Wu, Y. H.; Lu, M. Y.; Chen, M. Z.; Li, J. L.; Ma, J. P. OPUS-Ca: A knowledge-based potential function requiring only C alpha positions Protein Sci. 2007, 16 (7) 1449-1463
    • (2007) Protein Sci. , vol.16 , Issue.7 , pp. 1449-1463
    • Wu, Y.H.1    Lu, M.Y.2    Chen, M.Z.3    Li, J.L.4    Ma, J.P.5
  • 98
    • 77949462824 scopus 로고    scopus 로고
    • New statistical potential for quality assessment of protein models and a survey of energy functions
    • Rykunov, D.; Fiser, A. New statistical potential for quality assessment of protein models and a survey of energy functions BMC Bioinf. 2010, 11
    • (2010) BMC Bioinf. , pp. 11
    • Rykunov, D.1    Fiser, A.2
  • 99
    • 33750991346 scopus 로고    scopus 로고
    • Benchmarking sets for molecular docking
    • Huang, N.; Shoichet, B. K.; Irwin, J. J. Benchmarking sets for molecular docking J. Med. Chem. 2006, 49 (23) 6789-6801
    • (2006) J. Med. Chem. , vol.49 , Issue.23 , pp. 6789-6801
    • Huang, N.1    Shoichet, B.K.2    Irwin, J.J.3
  • 100
    • 33749578940 scopus 로고    scopus 로고
    • Statistical potential for assessment and prediction of protein structures
    • Shen, M. Y.; Sali, A. Statistical potential for assessment and prediction of protein structures Protein Sci. 2006, 15 (11) 2507-2524
    • (2006) Protein Sci. , vol.15 , Issue.11 , pp. 2507-2524
    • Shen, M.Y.1    Sali, A.2
  • 101
    • 0025341310 scopus 로고
    • Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins
    • Sippl, M. J. Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins J. Mol. Biol. 1990, 213 (4) 859-83
    • (1990) J. Mol. Biol. , vol.213 , Issue.4 , pp. 859-883
    • Sippl, M.J.1
  • 102
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali, A.; Blundell, T. L. Comparative protein modelling by satisfaction of spatial restraints J. Mol. Biol. 1993, 234 (3) 779-815
    • (1993) J. Mol. Biol. , vol.234 , Issue.3 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 104
    • 0031965676 scopus 로고    scopus 로고
    • Flexible ligand docking using conformational ensembles
    • Lorber, D. M.; Shoichet, B. K. Flexible ligand docking using conformational ensembles Protein Sci. 1998, 7 (4) 938-950
    • (1998) Protein Sci. , vol.7 , Issue.4 , pp. 938-950
    • Lorber, D.M.1    Shoichet, B.K.2
  • 105
    • 23844444239 scopus 로고    scopus 로고
    • Hierarchical docking of databases of multiple ligand conformations
    • Lorber, D. M.; Shoichet, B. K. Hierarchical docking of databases of multiple ligand conformations Curr. Top. Med. Chem. 2005, 5 (8) 739-749
    • (2005) Curr. Top. Med. Chem. , vol.5 , Issue.8 , pp. 739-749
    • Lorber, D.M.1    Shoichet, B.K.2
  • 108
    • 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 (3) 470-489
    • (1996) J. Mol. Biol. , vol.261 , Issue.3 , pp. 470-489
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.4
  • 110
    • 31544450787 scopus 로고    scopus 로고
    • Novel procedure for modeling ligand/receptor induced fit effects
    • Sherman, W.; Day, T.; Jacobson, M. P.; Friesner, R. A.; Farid, R. Novel procedure for modeling ligand/receptor induced fit effects J. Med. Chem. 2006, 49 (2) 534-553
    • (2006) J. Med. Chem. , vol.49 , Issue.2 , pp. 534-553
    • Sherman, W.1    Day, T.2    Jacobson, M.P.3    Friesner, R.A.4    Farid, R.5
  • 112
    • 47249097083 scopus 로고    scopus 로고
    • Customizing scoring functions for docking
    • Pham, T. A.; Jain, A. N. Customizing scoring functions for docking J. Comput.-Aided Mol. Des. 2008, 22 (5) 269-286
    • (2008) J. Comput.-Aided Mol. Des. , vol.22 , Issue.5 , pp. 269-286
    • Pham, T.A.1    Jain, A.N.2
  • 113
    • 33646740651 scopus 로고    scopus 로고
    • Parameter estimation for scoring protein-ligand interactions using negative training data
    • Pham, T. A.; Jain, A. N. Parameter estimation for scoring protein-ligand interactions using negative training data J. Med. Chem. 2006, 49 (20) 5856-5868
    • (2006) J. Med. Chem. , vol.49 , Issue.20 , pp. 5856-5868
    • Pham, T.A.1    Jain, A.N.2
  • 117
    • 80055002526 scopus 로고    scopus 로고
    • The Discovery of New Enzymes: Cytokinin Deaminase
    • Goble, A. M.; Fan, H.; Sali, A.; Raushel, F. M., The Discovery of New Enzymes: Cytokinin Deaminase. ACS Chem. Biol. 2011, 6 (10), 1036-1040.
    • (2011) ACS Chem. Biol. , vol.6 , Issue.10 , pp. 1036-1040
    • Goble, A.M.1    Fan, H.2    Sali, A.3    Raushel, F.M.4
  • 118
    • 0027136282 scopus 로고
    • Comparative Protein Modeling by Satisfaction of Spatial Restraints
    • Sali, A.; Blundell, T. L. Comparative Protein Modeling by Satisfaction of Spatial Restraints J. Mol. Biol. 1993, 234 (3) 779-815
    • (1993) J. Mol. Biol. , vol.234 , Issue.3 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 119
    • 0033810049 scopus 로고    scopus 로고
    • Modeling of loops in protein structures
    • Fiser, A.; Do, R. K. G.; Sali, A. Modeling of loops in protein structures Protein Sci. 2000, 9 (9) 1753-1773
    • (2000) Protein Sci. , vol.9 , Issue.9 , pp. 1753-1773
    • Fiser, A.1    Do, R.K.G.2    Sali, A.3
  • 120
    • 0007715651 scopus 로고
    • Structure of Chloramphenicol Acetyltransferase at 1.75-a Resolution
    • Leslie, A. G. W.; Moody, P. C. E.; Shaw, W. V. Structure of Chloramphenicol Acetyltransferase at 1.75-a Resolution Proc. Natl. Acad. Sci. U. S. A. 1988, 85 (12) 4133-4137
    • (1988) Proc. Natl. Acad. Sci. U. S. A. , vol.85 , Issue.12 , pp. 4133-4137
    • Leslie, A.G.W.1    Moody, P.C.E.2    Shaw, W.V.3
  • 121
    • 0025228570 scopus 로고
    • Evidence for Transition-State Stabilization by Serine-148 in the Catalytic Mechanism of Chloramphenicol Acetyltransferase
    • Lewendon, A.; Murray, I. A.; Shaw, W. V.; Gibbs, M. R.; Leslie, A. G. W. Evidence for Transition-State Stabilization by Serine-148 in the Catalytic Mechanism of Chloramphenicol Acetyltransferase Biochemistry (Mosc.) 1990, 29 (8) 2075-2080
    • (1990) Biochemistry (Mosc.) , vol.29 , Issue.8 , pp. 2075-2080
    • Lewendon, A.1    Murray, I.A.2    Shaw, W.V.3    Gibbs, M.R.4    Leslie, A.G.W.5
  • 122
    • 0032167901 scopus 로고    scopus 로고
    • Highly selective mechanism-based thrombin inhibitors: Structures of thrombin and trypsin inhibited with rigid peptidyl aldehydes
    • Krishnan, R.; Zhang, E.; Hakansson, K.; Arni, R. K.; Tulinsky, A.; Lim-Wilby, M. S. L.; Levy, O. E.; Semple, J. E.; Brunck, T. K. Highly selective mechanism-based thrombin inhibitors: Structures of thrombin and trypsin inhibited with rigid peptidyl aldehydes Biochemistry-Us 1998, 37 (35) 12094-12103
    • (1998) Biochemistry-Us , vol.37 , Issue.35 , pp. 12094-12103
    • Krishnan, R.1    Zhang, E.2    Hakansson, K.3    Arni, R.K.4    Tulinsky, A.5    Lim-Wilby, M.S.L.6    Levy, O.E.7    Semple, J.E.8    Brunck, T.K.9
  • 123
    • 0026775924 scopus 로고
    • Crystal-Structure of Chicken Liver Dihydrofolate-Reductase Complexed with Nadp+ and Biopterin
    • Mctigue, M. A.; Davies, J. F.; Kaufman, B. T.; Kraut, J. Crystal-Structure of Chicken Liver Dihydrofolate-Reductase Complexed with Nadp+ and Biopterin Biochemistry (Mosc.) 1992, 31 (32) 7264-7273
    • (1992) Biochemistry (Mosc.) , vol.31 , Issue.32 , pp. 7264-7273
    • McTigue, M.A.1    Davies, J.F.2    Kaufman, B.T.3    Kraut, J.4
  • 124
    • 0028519286 scopus 로고
    • Prediction of New Serine Proteinase-Inhibitors
    • Kurinov, I. V.; Harrison, R. W. Prediction of New Serine Proteinase-Inhibitors Nat. Struct. Biol. 1994, 1 (10) 735-743
    • (1994) Nat. Struct. Biol. , vol.1 , Issue.10 , pp. 735-743
    • Kurinov, I.V.1    Harrison, R.W.2
  • 125
    • 16844378060 scopus 로고    scopus 로고
    • Structure-based optimization of a non-beta-lactam lead results in inhibitors that do not up-regulate beta-lactamase expression in cell culture
    • Tondi, D.; Morandi, F.; Bonnet, R.; Costi, M. P.; Shoichet, B. K. Structure-based optimization of a non-beta-lactam lead results in inhibitors that do not up-regulate beta-lactamase expression in cell culture J. Am. Chem. Soc. 2005, 127 (13) 4632-4639
    • (2005) J. Am. Chem. Soc. , vol.127 , Issue.13 , pp. 4632-4639
    • Tondi, D.1    Morandi, F.2    Bonnet, R.3    Costi, M.P.4    Shoichet, B.K.5
  • 126
    • 0037130228 scopus 로고    scopus 로고
    • Structure-based approach for binding site identification on AmpC beta-lactamase
    • Powers, R. A.; Shoichet, B. K. Structure-based approach for binding site identification on AmpC beta-lactamase J. Med. Chem. 2002, 45 (15) 3222-3234
    • (2002) J. Med. Chem. , vol.45 , Issue.15 , pp. 3222-3234
    • Powers, R.A.1    Shoichet, B.K.2
  • 127
    • 0031450506 scopus 로고    scopus 로고
    • Hydrogen bonds and salt bridges across protein-protein interfaces
    • Xu, D.; Tsai, C. J.; Nussinov, R. Hydrogen bonds and salt bridges across protein-protein interfaces Protein Eng. 1997, 10 (9) 999-1012
    • (1997) Protein Eng. , vol.10 , Issue.9 , pp. 999-1012
    • Xu, D.1    Tsai, C.J.2    Nussinov, R.3


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