메뉴 건너뛰기




Volumn 50, Issue 10, 2010, Pages 1855-1864

Binding energy landscape analysis helps to discriminate true hits from high-scoring decoys in virtual screening

Author keywords

[No Author keywords available]

Indexed keywords

BINDERS; COMPLEXATION; LIGANDS; LOGISTIC REGRESSION; PROTEINS; STATISTICAL TESTS; THERMODYNAMIC STABILITY;

EID: 77958565592     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci900463u     Document Type: Article
Times cited : (21)

References (52)
  • 1
    • 33745199815 scopus 로고    scopus 로고
    • Virtual ligand screening: Strategies, perspectives and limitations
    • Klebe, G. Virtual ligand screening: strategies, perspectives and limitations Drug Discov. Today 2006, 11, 580-594
    • (2006) Drug Discov. Today , vol.11 , pp. 580-594
    • Klebe, G.1
  • 2
    • 8844263008 scopus 로고    scopus 로고
    • Docking and scoring in virtual screening for drug discovery: Methods and applications
    • Kitchen, D. B.; Decornez, H.; Furr, J. R.; Bajorath, J. Docking and scoring in virtual screening for drug discovery: Methods and applications Nat. Rev. Drug Discov. 2004, 3, 935-949
    • (2004) Nat. Rev. Drug Discov. , vol.3 , pp. 935-949
    • Kitchen, D.B.1    Decornez, H.2    Furr, J.R.3    Bajorath, J.4
  • 5
    • 22844440711 scopus 로고    scopus 로고
    • New and fast statistical-thermodynamic method for computation of protein-ligand binding entropy substantially improves docking accuracy
    • Ruvinsky, A. M.; Kozintsev, A. V. New and fast statistical-thermodynamic method for computation of protein-ligand binding entropy substantially improves docking accuracy J. Comput. Chem. 2005, 26, 1089-1095
    • (2005) J. Comput. Chem. , vol.26 , pp. 1089-1095
    • Ruvinsky, A.M.1    Kozintsev, A.V.2
  • 6
    • 34248358986 scopus 로고    scopus 로고
    • Role of binding entropy in the refinement of protein-ligand docking predictions: Analysis based on the use of 11 scoring functions
    • Ruvinsky, A. M. Role of binding entropy in the refinement of protein-ligand docking predictions: Analysis based on the use of 11 scoring functions J. Comput. Chem. 2007, 28, 1364-1372
    • (2007) J. Comput. Chem. , vol.28 , pp. 1364-1372
    • Ruvinsky, A.M.1
  • 7
    • 34547588237 scopus 로고    scopus 로고
    • Calculations of protein-ligand binding entropy of relative and overall molecular motions
    • Ruvinsky, A. M. Calculations of protein-ligand binding entropy of relative and overall molecular motions J. Comput.-Aided Mol. Des. 2007, 21, 361-370
    • (2007) J. Comput.-Aided Mol. Des. , vol.21 , pp. 361-370
    • Ruvinsky, A.M.1
  • 8
    • 0035011980 scopus 로고    scopus 로고
    • Protein ligand docking based on empirical method for binding affinity estimation
    • Tao, P.; Lai, L. H. Protein ligand docking based on empirical method for binding affinity estimation J. Comput.-Aided Mol. Des. 2001, 15, 429-446
    • (2001) J. Comput.-Aided Mol. Des. , vol.15 , pp. 429-446
    • Tao, P.1    Lai, L.H.2
  • 9
    • 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, 5856-5868
    • (2006) J. Med. Chem. , vol.49 , pp. 5856-5868
    • Pham, T.A.1    Jain, A.N.2
  • 10
    • 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
  • 12
    • 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
  • 13
    • 0038174853 scopus 로고    scopus 로고
    • Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening
    • Zavodszky, M. I.; Sanschagrin, P. C.; Korde, R. S.; Kuhn, L. A. Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening J. Comput.-Aided Mol. Des. 2002, 16, 883-902
    • (2002) J. Comput.-Aided Mol. Des. , vol.16 , pp. 883-902
    • Zavodszky, M.I.1    Sanschagrin, P.C.2    Korde, R.S.3    Kuhn, L.A.4
  • 15
    • 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
  • 16
    • 33747200808 scopus 로고    scopus 로고
    • Combining docking and molecular dynamic simulations in drug design
    • Alonso, H.; Bliznyuk, A. A.; Gready, J. E. Combining docking and molecular dynamic simulations in drug design Med. Res. Rev. 2006, 26, 531-568
    • (2006) Med. Res. Rev. , vol.26 , pp. 531-568
    • Alonso, H.1    Bliznyuk, A.A.2    Gready, J.E.3
  • 17
    • 33645400172 scopus 로고    scopus 로고
    • A multistep approach to structure-based drug design: Studying ligand binding at the human neutrophil elastase
    • Steinbrecher, T.; Case, D. A.; Labahn, A. A multistep approach to structure-based drug design: Studying ligand binding at the human neutrophil elastase J. Med. Chem. 2006, 49, 1837-1844
    • (2006) J. Med. Chem. , vol.49 , pp. 1837-1844
    • Steinbrecher, T.1    Case, D.A.2    Labahn, A.3
  • 19
    • 20444410410 scopus 로고    scopus 로고
    • Virtual screening of molecular databases using a support vector machine
    • Jorissen, R. N.; Gilson, M. K. Virtual screening of molecular databases using a support vector machine J. Chem. Inf. Model. 2005, 45, 549-561
    • (2005) J. Chem. Inf. Model. , vol.45 , pp. 549-561
    • Jorissen, R.N.1    Gilson, M.K.2
  • 20
    • 33846212271 scopus 로고    scopus 로고
    • Comparison of shape-matching and docking as virtual screening tools
    • Hawkins, P. C. D.; Skillman, A. G.; Nicholls, A. Comparison of shape-matching and docking as virtual screening tools J. Med. Chem. 2007, 50, 74-82
    • (2007) J. Med. Chem. , vol.50 , pp. 74-82
    • Hawkins, P.C.D.1    Skillman, A.G.2    Nicholls, A.3
  • 21
    • 13844320566 scopus 로고    scopus 로고
    • LigandScout: 3-d pharmacophores derived from protein-bound ligands and their use as virtual screening filters
    • Wolber, G.; Langer, T. LigandScout: 3-d pharmacophores derived from protein-bound ligands and their use as virtual screening filters J. Chem. Inf. Model. 2005, 45, 160-169
    • (2005) J. Chem. Inf. Model. , vol.45 , pp. 160-169
    • Wolber, G.1    Langer, T.2
  • 22
    • 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, 6821-6831
    • (2005) J. Med. Chem. , vol.48 , pp. 6821-6831
    • Springer, C.1    Adalsteinsson, H.2    Young, M.M.3    Kegelmeyer, P.W.4    Roe, D.C.5
  • 24
    • 7044239742 scopus 로고
    • Free-Energy Calculations: Applications to Chemical and Biochemical Phenomena
    • Kollman, P. Free-Energy Calculations: Applications to Chemical and Biochemical Phenomena Chem. Rev. 1993, 93, 2395-2417
    • (1993) Chem. Rev. , vol.93 , pp. 2395-2417
    • Kollman, P.1
  • 27
    • 0027234766 scopus 로고
    • Engineering of Stable and Fast-Folding Sequences of Model Proteins
    • Shakhnovich, E. I.; Gutin, A. M. Engineering of Stable and Fast-Folding Sequences of Model Proteins Proc. Natl. Acad. Sci. U S A. 1993, 90, 7195-7199
    • (1993) Proc. Natl. Acad. Sci. U S A. , vol.90 , pp. 7195-7199
    • Shakhnovich, E.I.1    Gutin, A.M.2
  • 28
    • 4243392673 scopus 로고
    • Proteins with Selected Sequences Fold into Unique Native Conformation
    • Shakhnovich, E. I. Proteins with Selected Sequences Fold into Unique Native Conformation Phys. Rev. Lett. 1994, 72, 3907-3910
    • (1994) Phys. Rev. Lett. , vol.72 , pp. 3907-3910
    • Shakhnovich, E.I.1
  • 29
    • 0028270634 scopus 로고
    • Kinetics of Protein Folding. A Lattice Model Study of the Requirements for Folding to the Native State
    • Sali, A.; Shakhnovich, E.; Karplus, M. Kinetics of Protein Folding. A Lattice Model Study of the Requirements for Folding to the Native State J. Mol. Biol. 1994, 235, 1614-1636
    • (1994) J. Mol. Biol. , vol.235 , pp. 1614-1636
    • Sali, A.1    Shakhnovich, E.2    Karplus, M.3
  • 32
    • 0028947257 scopus 로고
    • Funnels, Pathways, and the Energy Landscape of Protein Folding: A Synthesis
    • Bryngelson, J. D.; Onuchic, J. N.; Socci, N. D.; Wolynes, P. G. Funnels, Pathways, and the Energy Landscape of Protein Folding: A Synthesis Proteins 1995, 21, 167-195
    • (1995) Proteins , vol.21 , pp. 167-195
    • Bryngelson, J.D.1    Onuchic, J.N.2    Socci, N.D.3    Wolynes, P.G.4
  • 36
    • 0030055657 scopus 로고    scopus 로고
    • Exploring the energy landscapes of molecular recognition by a genetic algorithm: Analysis of the requirements for robust docking of HIV-1 protease and FKRP-12 complexes
    • Verkhivker, G. M.; Rejto, P. A.; Gehlhaar, D. K.; Freer, S. T. Exploring the energy landscapes of molecular recognition by a genetic algorithm: Analysis of the requirements for robust docking of HIV-1 protease and FKRP-12 complexes Proteins 1996, 25, 342-353
    • (1996) Proteins , vol.25 , pp. 342-353
    • Verkhivker, G.M.1    Rejto, P.A.2    Gehlhaar, D.K.3    Freer, S.T.4
  • 37
    • 0029829066 scopus 로고    scopus 로고
    • Unraveling principles of lead discovery: From unfrustrated energy landscapes to novel molecular anchors
    • Rejto, P. A.; Verkhivker, G. M. Unraveling principles of lead discovery: From unfrustrated energy landscapes to novel molecular anchors Proc. Natl. Acad. Sci. U S A. 1996, 93, 8945-8950
    • (1996) Proc. Natl. Acad. Sci. U S A. , vol.93 , pp. 8945-8950
    • Rejto, P.A.1    Verkhivker, G.M.2
  • 38
    • 0030058373 scopus 로고    scopus 로고
    • A mean field model of ligand protein interactions: Implications for the structural assessment of human immunodeficiency virus type 1 protease complexes and receptor-specific binding
    • Verkhivker, G. M.; Rejto, P. A. A mean field model of ligand protein interactions: Implications for the structural assessment of human immunodeficiency virus type 1 protease complexes and receptor-specific binding Proc. Natl. Acad. Sci. U S A. 1996, 93, 60-64
    • (1996) Proc. Natl. Acad. Sci. U S A. , vol.93 , pp. 60-64
    • Verkhivker, G.M.1    Rejto, P.A.2
  • 39
    • 0038266221 scopus 로고    scopus 로고
    • Energy landscape theory, funnels, specificity, and optimal criterion of biomolecular binding
    • Wang, J.; Verkhivker, G. M. Energy landscape theory, funnels, specificity, and optimal criterion of biomolecular binding Phys. Rev. Lett. 2003, 90, 188101-188104
    • (2003) Phys. Rev. Lett. , vol.90 , pp. 188101-188104
    • Wang, J.1    Verkhivker, G.M.2
  • 40
    • 35948986361 scopus 로고    scopus 로고
    • Quantifying intrinsic specificity: A potential complement to affinity in drug screening
    • Wang, J.; Zheng, X.; Yang, Y.; Drueckhammer, D.; Yang, W.; Verkhivker, G.; Wang, E. Quantifying intrinsic specificity: A potential complement to affinity in drug screening Phys. Rev. Lett. 2007, 99, 198101-198104
    • (2007) Phys. Rev. Lett. , vol.99 , pp. 198101-198104
    • Wang, J.1    Zheng, X.2    Yang, Y.3    Drueckhammer, D.4    Yang, W.5    Verkhivker, G.6    Wang, E.7
  • 41
    • 2942519283 scopus 로고    scopus 로고
    • Assessment of multiple binding modes in ligand-protein docking
    • Kallblad, P.; Mancera, R. L.; Todorov, N. P. Assessment of multiple binding modes in ligand-protein docking J. Med. Chem. 2004, 47, 3334-3337
    • (2004) J. Med. Chem. , vol.47 , pp. 3334-3337
    • Kallblad, P.1    Mancera, R.L.2    Todorov, N.P.3
  • 42
    • 1542319916 scopus 로고    scopus 로고
    • Cooperativity principles in protein folding
    • Chan, H. S.; Shimizu, S.; Kaya, H. Cooperativity principles in protein folding Methods Enzymol. 2004, 380, 350-379
    • (2004) Methods Enzymol. , vol.380 , pp. 350-379
    • Chan, H.S.1    Shimizu, S.2    Kaya, H.3
  • 43
    • 0026345750 scopus 로고
    • Folding of Chymotrypsin Inhibitor-2. 1. Evidence for a Two-State Transition
    • Jackson, S. E.; Fersht, A. R. Folding of Chymotrypsin Inhibitor-2. 1. Evidence for a Two-State Transition Biochemistry 1991, 30, 10428-10435
    • (1991) Biochemistry , vol.30 , pp. 10428-10435
    • Jackson, S.E.1    Fersht, A.R.2
  • 44
    • 0034604105 scopus 로고    scopus 로고
    • A surprising simplicity to protein folding
    • Baker, D. A surprising simplicity to protein folding Nature 2000, 405, 39-42
    • (2000) Nature , vol.405 , pp. 39-42
    • Baker, D.1
  • 46
    • 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, 6789-6801
    • (2006) J. Med. Chem. , vol.49 , pp. 6789-6801
    • Huang, N.1    Shoichet, B.K.2    Irwin, J.J.3
  • 47
    • 41449114598 scopus 로고    scopus 로고
    • Community benchmarks for virtual screening
    • Irwin, J. J. Community benchmarks for virtual screening J. Comput.-Aided Mol. Des. 2008, 22, 193-199
    • (2008) J. Comput.-Aided Mol. Des. , vol.22 , pp. 193-199
    • Irwin, J.J.1
  • 48
    • 0036074173 scopus 로고    scopus 로고
    • Fast-folding protein kinetics, hidden intermediates, and the sequential stabilization model
    • Ozkan, S. B.; Dill, K. A.; Bahar, I. Fast-folding protein kinetics, hidden intermediates, and the sequential stabilization model Protein Sci. 2002, 11, 1958-1970
    • (2002) Protein Sci. , vol.11 , pp. 1958-1970
    • Ozkan, S.B.1    Dill, K.A.2    Bahar, I.3
  • 49
    • 31444452031 scopus 로고    scopus 로고
    • P versus Q: Structural reaction coordinates capture protein folding on smooth landscapes
    • Cho, S. S.; Levy, Y.; Wolynes, P. G. P versus Q: Structural reaction coordinates capture protein folding on smooth landscapes Proc. Natl. Acad. Sci. U S A. 2006, 103, 586-591
    • (2006) Proc. Natl. Acad. Sci. U S A. , vol.103 , pp. 586-591
    • Cho, S.S.1    Levy, Y.2    Wolynes, P.G.3
  • 50
    • 6944235051 scopus 로고    scopus 로고
    • Hidden complexity of free energy surfaces for peptide (protein) folding
    • Krivov, S. V.; Karplus, M. Hidden complexity of free energy surfaces for peptide (protein) folding Proc. Natl. Acad. Sci. U S A. 2004, 101, 14766-14770
    • (2004) Proc. Natl. Acad. Sci. U S A. , vol.101 , pp. 14766-14770
    • Krivov, S.V.1    Karplus, M.2
  • 51
    • 33646931471 scopus 로고    scopus 로고
    • Protein folding thermodynamics and dynamics: Where physics, chemistry, and biology meet
    • Shakhnovich, E. Protein folding thermodynamics and dynamics: Where physics, chemistry, and biology meet Chem. Rev. 2006, 106, 1559-1588
    • (2006) Chem. Rev. , vol.106 , pp. 1559-1588
    • Shakhnovich, E.1
  • 52
    • 0001704085 scopus 로고    scopus 로고
    • SCORE: A new empirical method for estimating the binding affinity of a protein-ligand complex
    • Wang, R. X.; Liu, L.; Lai, L. H.; Tang, Y. Q. 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.X.1    Liu, L.2    Lai, L.H.3    Tang, Y.Q.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.