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Volumn 30, Issue 12, 2014, Pages 1674-1680

Improved protein-ligand binding affinity prediction by using a curvature-dependent surface-area model

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; PROTEIN;

EID: 84902438255     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu104     Document Type: Article
Times cited : (139)

References (64)
  • 1
    • 38849196324 scopus 로고    scopus 로고
    • Water as an active constituent in cell biology
    • Ball, P. (2007) Water as an active constituent in cell biology. Chem. Rev., 108, 74-108.
    • (2007) Chem. Rev. , vol.108 , pp. 74-108
    • Ball, P.1
  • 2
    • 77952825581 scopus 로고    scopus 로고
    • A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking
    • Ballester, P.J. and Mitchell, J.B. (2010) A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking. Bioinformatics, 26, 1169-1175.
    • (2010) Bioinformatics , vol.26 , pp. 1169-1175
    • Ballester, P.J.1    Mitchell, J.B.2
  • 3
  • 4
    • 0030574268 scopus 로고    scopus 로고
    • Structure-based drug design
    • Blundell, T.L. (1996) Structure-based drug design. Nature, 384(Suppl 6604), 23-26.
    • (1996) Nature , vol.384 , Issue.SUPPL. 6604 , pp. 23-26
    • Blundell, T.L.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
    • Bohm, H.J. (1998) 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., 12, 309-323.
    • (1998) J. Comput. Aided Mol. Des. , vol.12 , pp. 309-323
    • Bohm, H.J.1
  • 6
    • 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
    • Bohm, H.J. (1994) 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., 8, 243-256.
    • (1994) J. Comput. Aided Mol. Des. , vol.8 , pp. 243-256
    • Bohm, H.J.1
  • 7
    • 84986512474 scopus 로고
    • CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
    • Brooks, B. et al. (1983) CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem., 4, 187-217.
    • (1983) J. Comput. Chem. , vol.4 , pp. 187-217
    • Brooks, B.1
  • 8
    • 26944481188 scopus 로고    scopus 로고
    • Interfaces and the driving force of hydrophobic assembly
    • Chandler, D. (2005) Interfaces and the driving force of hydrophobic assembly. Nature, 437, 640-647.
    • (2005) Nature , vol.437 , pp. 640-647
    • Chandler, D.1
  • 9
    • 0032537184 scopus 로고    scopus 로고
    • Surface topography dependence of biomolecu-lar hydrophobic hydration
    • Cheng, Y.K. and Rossky, P.J. (1998) Surface topography dependence of biomolecu-lar hydrophobic hydration. Nature 1998, 392, 696-699.
    • (1998) Nature 1998 , vol.392 , pp. 696-699
    • Cheng, Y.K.1    Rossky, P.J.2
  • 10
    • 66149103553 scopus 로고    scopus 로고
    • Comparative assessment of scoring functions on a diverse test set
    • Cheng, T. et al. (2009) Comparative assessment of scoring functions on a diverse test set. J. Chem. Inf. Model, 49, 1079-1093.
    • (2009) J. Chem. Inf. Model , vol.49 , pp. 1079-1093
    • Cheng, T.1
  • 11
    • 0017187836 scopus 로고
    • The nature of the accessible and buried surfaces in proteins
    • Chothia, C. (1976) The nature of the accessible and buried surfaces in proteins. J. Mol. Biol., 105, 1-12.
    • (1976) J. Mol. Biol. , vol.105 , pp. 1-12
    • Chothia, C.1
  • 12
    • 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. et al. (1997) 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., 11, 425-445.
    • (1997) J. Comput. Aided Mol. Des. , vol.11 , pp. 425-445
    • Eldridge, M.D.1
  • 13
    • 0035025191 scopus 로고    scopus 로고
    • DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
    • Ewing, T.J. et al. (2001) DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J. Comput. Aided Mol. Des., 15, 411-428.
    • (2001) J. Comput. Aided Mol. Des. , vol.15 , pp. 411-428
    • Ewing, T.J.1
  • 14
    • 74849120001 scopus 로고    scopus 로고
    • Oil/water transfer is partly driven by molecular shape, not just size
    • Fennell, C.J. et al. (2010) Oil/water transfer is partly driven by molecular shape, not just size. J. Am. Chem. Soc., 132, 234-240.
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 234-240
    • Fennell, C.J.1
  • 15
    • 36849117971 scopus 로고
    • Free volume and entropy in condensed systems III. Entropy in binary liquid mixtures; Partial molal entropy in dilute solutions; Structure and thermodynamics in aqueous electrolytes
    • Frank, H. and Evans, M. (1945) Free volume and entropy in condensed systems III. Entropy in binary liquid mixtures; partial molal entropy in dilute solutions; structure and thermodynamics in aqueous electrolytes. J. Chem. Phys., 13, 507-532.
    • (1945) J. Chem. Phys. , vol.13 , pp. 507-532
    • Frank, H.1    Evans, M.2
  • 16
    • 33750124980 scopus 로고    scopus 로고
    • Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes
    • Friesner, R.A. et al. (2006) Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J. Med. Chem., 49, 6177-6196.
    • (2006) J. Med. Chem. , vol.49 , pp. 6177-6196
    • Friesner, R.A.1
  • 17
    • 12144289984 scopus 로고    scopus 로고
    • Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
    • Friesner, R.A. et al. (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J. Med. Chem., 47, 1739-1749.
    • (2004) J. Med. Chem. , vol.47 , pp. 1739-1749
    • Friesner, R.A.1
  • 18
    • 0029294584 scopus 로고
    • Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: Conformationally flexible docking by evolutionary programming
    • Gehlhaar, D.K. et al. (1995) Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming. Chem. Biol., 2, 317-324.
    • (1995) Chem. Biol. , vol.2 , pp. 317-324
    • Gehlhaar, D.K.1
  • 19
    • 0034645763 scopus 로고    scopus 로고
    • Knowledge-based scoring function to predict protein-ligand interactions
    • Gohlke, H. et al. (2000) Knowledge-based scoring function to predict protein-ligand interactions. J. Mol. Biol., 295, 337-356.
    • (2000) J. Mol. Biol. , vol.295 , pp. 337-356
    • Gohlke, H.1
  • 20
    • 0021871375 scopus 로고
    • A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
    • Goodford, P.J. (1985) A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem., 28, 849-857.
    • (1985) J. Med. Chem. , vol.28 , pp. 849-857
    • Goodford, P.J.1
  • 21
    • 0141560569 scopus 로고    scopus 로고
    • Entropy convergence in hydrophobic hydration: A scaled particle theory analysis
    • Graziano, G. and Lee, B. (2003) Entropy convergence in hydrophobic hydration: a scaled particle theory analysis. Biophys. Chem., 105, 241-250.
    • (2003) Biophys. Chem. , vol.105 , pp. 241-250
    • Graziano, G.1    Lee, B.2
  • 22
    • 77649221514 scopus 로고    scopus 로고
    • Inclusion of solvation and entropy in the knowledge-based scoring function for protein-ligand interactions
    • Huang, S.Y. and Zou, X. (2010) Inclusion of solvation and entropy in the knowledge-based scoring function for protein-ligand interactions. J. Chem. Inf. Model, 50, 262-273.
    • (2010) J. Chem. Inf. Model , vol.50 , pp. 262-273
    • Huang, S.Y.1    Zou, X.2
  • 23
    • 77957898063 scopus 로고    scopus 로고
    • Scoring functions and their evaluation methods for pro-tein-ligand docking: Recent advances and future directions
    • Huang, S.-Y. et al. (2010) Scoring functions and their evaluation methods for pro-tein-ligand docking: recent advances and future directions. Phys. Chem., 12, 12899-12908.
    • (2010) Phys. Chem. , vol.12 , pp. 12899-12908
    • Huang, S.-Y.1
  • 24
    • 0030255303 scopus 로고    scopus 로고
    • Scoring noncovalent protein-ligand interactions: A continuous dif-ferentiable function tuned to compute binding affinities
    • Jain, A.N. (1996) Scoring noncovalent protein-ligand interactions: a continuous dif-ferentiable function tuned to compute binding affinities. J. Comput. Aided Mol. Des., 10, 427-440.
    • (1996) J. Comput. Aided Mol. Des. , vol.10 , pp. 427-440
    • Jain, A.N.1
  • 25
    • 0008863560 scopus 로고
    • Some factors in the interpretation of protein denaturation
    • Kauzmann, W. (1959) Some factors in the interpretation of protein denaturation. Adv. Protein chem., 14, 1-63.
    • (1959) Adv. Protein Chem. , vol.14 , pp. 1-63
    • Kauzmann, W.1
  • 26
    • 0031673012 scopus 로고    scopus 로고
    • Efficient collision detection using bounding volume hierarchies of k-DOPs
    • Klosowski, J.T. et al. (1998) Efficient collision detection using bounding volume hierarchies of k-DOPs. IEEE Trans. Visual. Comput. Graph., 4, 21-36.
    • (1998) IEEE Trans. Visual. Comput. Graph. , vol.4 , pp. 21-36
    • Klosowski, J.T.1
  • 27
    • 84883247468 scopus 로고    scopus 로고
    • Lessons learned in empirical scoring with smina from the CSAR 2011 benchmarking exercise
    • Koes, D.R., Baumgartner, M.P. and Camacho, C.J. (2013) Lessons learned in empirical scoring with smina from the CSAR 2011 benchmarking exercise. J. Chem. Inf. Model, 53, 1893-1904.
    • (2013) J. Chem. Inf. Model , vol.53 , pp. 1893-1904
    • Koes, D.R.1    Baumgartner, M.P.2    Camacho, C.J.3
  • 28
    • 62449330667 scopus 로고    scopus 로고
    • Empirical scoring functions for advanced protein-ligand docking with PLANTS
    • Korb, O. et al. (2009) Empirical scoring functions for advanced protein-ligand docking with PLANTS. J. Chem. Inf. Model, 49, 84-96.
    • (2009) J. Chem. Inf. Model , vol.49 , pp. 84-96
    • Korb, O.1
  • 29
    • 15244346501 scopus 로고    scopus 로고
    • LigScore: A novel scoring function for predicting binding affinities
    • Krammer, A. et al. (2005) LigScore: a novel scoring function for predicting binding affinities. J. Mol. Graph Model, 23, 395-407.
    • (2005) J. Mol. Graph Model , vol.23 , pp. 395-407
    • Krammer, A.1
  • 30
    • 0026730489 scopus 로고
    • Structure-based strategies for drug design and discovery
    • Kuntz, I.D. (1992) Structure-based strategies for drug design and discovery. Science, 257, 1078-1082.
    • (1992) Science , vol.257 , pp. 1078-1082
    • Kuntz, I.D.1
  • 31
    • 33744821352 scopus 로고    scopus 로고
    • Electrostatics of ligand binding: Parametrization of the generalized Born model and comparison with the Poisson-Boltzmann approach
    • Liu, H.Y. and Zou, X. (2006) Electrostatics of ligand binding: parametrization of the generalized Born model and comparison with the Poisson-Boltzmann approach. J. Phys. Chem. B, 110, 9304-9313.
    • (2006) J. Phys. Chem. B , vol.110 , pp. 9304-9313
    • Liu, H.Y.1    Zou, X.2
  • 32
    • 0011960339 scopus 로고    scopus 로고
    • Hydrophobicity at small and large length scales
    • Lum, K. et al. (1999) Hydrophobicity at small and large length scales. J. Phys. Chem. B, 103, 4570-4577.
    • (1999) J. Phys. Chem. B , vol.103 , pp. 4570-4577
    • Lum, K.1
  • 33
    • 0242417008 scopus 로고    scopus 로고
    • Interactions with aromatic rings in chemical and biological recognition
    • Meyer, E. et al. (2003) Interactions with aromatic rings in chemical and biological recognition. Angewandte Chemie International Edition, 42, 1210-1250.
    • (2003) Angewandte Chemie International Edition , vol.42 , pp. 1210-1250
    • Meyer, E.1
  • 34
    • 26444468103 scopus 로고    scopus 로고
    • General and targeted statistical potentials for protein-ligand interactions
    • Mooij, W.T. and Verdonk, M.L. (2005) General and targeted statistical potentials for protein-ligand interactions. Proteins, 61, 272-287.
    • (2005) Proteins , vol.61 , pp. 272-287
    • Mooij, W.T.1    Verdonk, M.L.2
  • 35
    • 0030203710 scopus 로고    scopus 로고
    • Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4
    • Morris, G.M. et al. (1996) Distributed automated docking of flexible ligands to proteins: parallel applications of AutoDock 2.4. J. Comput. Aided Mol. Des., 10, 293-304.
    • (1996) J. Comput. Aided Mol. Des. , vol.10 , pp. 293-304
    • Morris, G.M.1
  • 36
    • 33845873363 scopus 로고    scopus 로고
    • Development and validation of a modular, extensible docking program: DOCK 5
    • Moustakas, D.T. et al. (2006) Development and validation of a modular, extensible docking program: DOCK 5. J. Comput. Aided Mol. Des., 20, 601-619.
    • (2006) J. Comput. Aided Mol. Des. , vol.20 , pp. 601-619
    • Moustakas, D.T.1
  • 37
    • 33749242403 scopus 로고    scopus 로고
    • PMF scoring revisited
    • Muegge, I. (2006) PMF scoring revisited. J. Med. Chem., 49, 5895-5902.
    • (2006) J. Med. Chem. , vol.49 , pp. 5895-5902
    • Muegge, I.1
  • 38
    • 0033545622 scopus 로고    scopus 로고
    • A general and fast scoring function for protein-ligand interactions: A simplified potential approach
    • Muegge, I. and Martin, Y.C. (1999) A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J. Med. Chem., 42, 791-804.
    • (1999) J. Med. Chem. , vol.42 , pp. 791-804
    • Muegge, I.1    Martin, Y.C.2
  • 39
    • 80054943835 scopus 로고    scopus 로고
    • DSX: A knowledge-based scoring function for the assessment of protein-ligand complexes
    • Neudert, G. and Klebe, G. (2011) DSX: a knowledge-based scoring function for the assessment of protein-ligand complexes. J. Chem. Inf. Model, 51, 2731-2745.
    • (2011) J. Chem. Inf. Model , vol.51 , pp. 2731-2745
    • Neudert, G.1    Klebe, G.2
  • 40
    • 0026319199 scopus 로고
    • Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons
    • Nicholls, A. et al. (1991) Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins, 11, 281-296.
    • (1991) Proteins , vol.11 , pp. 281-296
    • Nicholls, A.1
  • 41
    • 0034486196 scopus 로고    scopus 로고
    • Free energy determinants of tertiary structure and the evaluation of protein models
    • Petrey, D. and Honig, B. (2000) Free energy determinants of tertiary structure and the evaluation of protein models. Protein Sci., 9, 2181-2191.
    • (2000) Protein Sci. , vol.9 , pp. 2181-2191
    • Petrey, D.1    Honig, B.2
  • 42
    • 36749120002 scopus 로고
    • Theory of the hydrophobic effect
    • Pratt, L. and Chandler, D. (1977) Theory of the hydrophobic effect. J. Chem. Phys., 67, 3683-3704.
    • (1977) J. Chem. Phys. , vol.67 , pp. 3683-3704
    • Pratt, L.1    Chandler, D.2
  • 43
    • 22144481993 scopus 로고    scopus 로고
    • Hydrophobic hydration from small to large lengthscales: Understanding and manipulating the crossover
    • Rajamani, S. et al. (2005) Hydrophobic hydration from small to large lengthscales: Understanding and manipulating the crossover. Proc. Natl Acad. Sci. USA, 102, 9475-9480.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 9475-9480
    • Rajamani, S.1
  • 44
    • 33845986373 scopus 로고    scopus 로고
    • Critical evaluation of methods to incorporate entropy loss upon binding in high-throughput docking
    • Salaniwal, S. et al. (2007) Critical evaluation of methods to incorporate entropy loss upon binding in high-throughput docking. Proteins, 66, 422-435.
    • (2007) Proteins , vol.66 , pp. 422-435
    • Salaniwal, S.1
  • 45
    • 70350751573 scopus 로고    scopus 로고
    • Dewetting-controlled binding of ligands to hydrophobic pockets
    • Setny, P. et al. (2009) Dewetting-controlled binding of ligands to hydrophobic pockets. Phys. Rev. Lett., 103, 187801.
    • (2009) Phys. Rev. Lett. , vol.103 , pp. 187801
    • Setny, P.1
  • 46
    • 0026416668 scopus 로고
    • Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects
    • Sharp, K.A. et al. (1991) Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects. Science, 252, 106-109.
    • (1991) Science , vol.252 , pp. 106-109
    • Sharp, K.A.1
  • 47
    • 0032939345 scopus 로고    scopus 로고
    • Ligand solvation in molecular docking
    • Shoichet, B.K. et al. (1999) Ligand solvation in molecular docking. Proteins, 34, 4-16.
    • (1999) Proteins , vol.34 , pp. 4-16
    • Shoichet, B.K.1
  • 48
    • 0015866154 scopus 로고
    • Environment and exposure to solvent of protein atoms. Lysozyme and insulin
    • Shrake, A. and Rupley, J.A. (1973) Environment and exposure to solvent of protein atoms. Lysozyme and insulin. J. Mol. Biol., 79, 351-371.
    • (1973) J. Mol. Biol. , vol.79 , pp. 351-371
    • Shrake, A.1    Rupley, J.A.2
  • 49
    • 0001764065 scopus 로고
    • Microscopic surface tension down to molecular dimensions and microthermodynamic surface areas of molecules or clusters
    • Sinanoglu, O. (1981) Microscopic surface tension down to molecular dimensions and microthermodynamic surface areas of molecules or clusters. J. Chem. Phys., 75, 463-468.
    • (1981) J. Chem. Phys. , vol.75 , pp. 463-468
    • Sinanoglu, O.1
  • 50
    • 84900467715 scopus 로고    scopus 로고
    • Is it the shape of the cavity, or the shape of the water in the cavity?
    • Snyder, P. et al. (2013) Is it the shape of the cavity, or the shape of the water in the cavity? Eur. Phys. J. Spec. Top., 1-39.
    • (2013) Eur. Phys. J. Spec. Top , pp. 1-39
    • Snyder, P.1
  • 51
    • 81055130316 scopus 로고    scopus 로고
    • Mechanism of the hydrophobic effect in the biomolecular recognition of arylsulfonamides by carbonic anhydrase
    • Snyder, P.W. et al. (2011) Mechanism of the hydrophobic effect in the biomolecular recognition of arylsulfonamides by carbonic anhydrase. Proc. Natl Acad. Sci. USA, 108, 17889-17894.
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , pp. 17889-17894
    • Snyder, P.W.1
  • 52
    • 0037165448 scopus 로고    scopus 로고
    • A view of the hydrophobic effect
    • Southall, N. et al. (2001) A view of the hydrophobic effect. J. Phys. Chem. B, 106, 521-533.
    • (2001) J. Phys. Chem. B , vol.106 , pp. 521-533
    • Southall, N.1
  • 53
    • 34250434907 scopus 로고
    • Structure in aqueous solutions of nonpolar solutes from the standpoint of scaled-particle theory
    • Stillinger, F. (1973) Structure in aqueous solutions of nonpolar solutes from the standpoint of scaled-particle theory. J. Sol. Chem., 2, 141-158.
    • (1973) J. Sol. Chem. , vol.2 , pp. 141-158
    • Stillinger, F.1
  • 54
    • 0018318966 scopus 로고
    • Interfacial free energy and the hydrophobic effect
    • Tanford, C. (1979) Interfacial free energy and the hydrophobic effect. Proc. Natl Acad. Sci. USA, 76, 4175-4176.
    • (1979) Proc. Natl Acad. Sci. USA , vol.76 , pp. 4175-4176
    • Tanford, C.1
  • 55
    • 79952148691 scopus 로고    scopus 로고
    • PHOENIX: A scoring function for affinity prediction derived using high-resolution crystal structures and calorimetry measurements
    • Tang, Y.T. and Marshall, G.R. (2011) PHOENIX: a scoring function for affinity prediction derived using high-resolution crystal structures and calorimetry measurements. J. Chem. Inf. Model, 51, 214-228.
    • (2011) J. Chem. Inf. Model , vol.51 , pp. 214-228
    • Tang, Y.T.1    Marshall, G.R.2
  • 56
    • 34147162778 scopus 로고
    • The effect of droplet size on surface tension
    • Tolman, R.C. (1949) The effect of droplet size on surface tension. J. Chem. Phys., 17, 5.
    • (1949) J. Chem. Phys. , vol.17 , pp. 5
    • Tolman, R.C.1
  • 57
    • 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. et al. (2005) 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., 48, 6296-6303.
    • (2005) J. Med. Chem. , vol.48 , pp. 6296-6303
    • Velec, H.F.1
  • 58
    • 0036022960 scopus 로고    scopus 로고
    • Further development and validation of empirical scoring functions for structure-based binding affinity prediction
    • Wang, R. et al. (2002) Further development and validation of empirical scoring functions for structure-based binding affinity prediction. J. Comput. Aided Mol. Des., 16, 11-26.
    • (2002) J. Comput. Aided Mol. Des. , vol.16 , pp. 11-26
    • Wang, R.1
  • 59
    • 2542530042 scopus 로고    scopus 로고
    • The PDBbind database: Collection of binding affinities for protein-ligand complexes with known three-dimensional structures
    • Wang, R. et al. (2004) The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures. J. Med. Chem., 47, 2977-2980.
    • (2004) J. Med. Chem. , vol.47 , pp. 2977-2980
    • Wang, R.1
  • 60
    • 20444422149 scopus 로고    scopus 로고
    • The PDBbind database: Methodologies and updates
    • Wang, R. et al. (2005) The PDBbind database: methodologies and updates. J. Med. Chem., 48, 4111-4119.
    • (2005) J. Med. Chem. , vol.48 , pp. 4111-4119
    • Wang, R.1
  • 61
    • 0036382728 scopus 로고    scopus 로고
    • A model binding site for testing scoring functions in molecular docking
    • Wei, B.Q. et al. (2002) A model binding site for testing scoring functions in molecular docking. J. Mol. Biol., 322, 339-355.
    • (2002) J. Mol. Biol. , vol.322 , pp. 339-355
    • Wei, B.Q.1
  • 62
    • 17144383951 scopus 로고    scopus 로고
    • A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes
    • Zhang, C. et al. (2005) A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes. J. Med. Chem., 48, 2325-2335.
    • (2005) J. Med. Chem. , vol.48 , pp. 2325-2335
    • Zhang, C.1
  • 63
    • 84878201814 scopus 로고    scopus 로고
    • Development of the knowledge-based and empirical combined scoring algorithm (kecsa) to score protein-ligand interactions
    • Zheng, Z. and Merz, K.M. Jr (2013) Development of the knowledge-based and empirical combined scoring algorithm (kecsa) to score protein-ligand interactions. J. Chem. Inf. Model, 53, 1073-1083.
    • (2013) J. Chem. Inf. Model , vol.53 , pp. 1073-1083
    • Zheng, Z.1    Merz, Jr.K.M.2
  • 64
    • 80054694711 scopus 로고    scopus 로고
    • GOAP: A generalized orientation-dependent, allatom statistical potential for protein structure prediction
    • Zhou, H. and Skolnick, J. (2011) GOAP: a generalized orientation- dependent, allatom statistical potential for protein structure prediction. Biophys. J., 101, 2043-2052.
    • (2011) Biophys. J. , vol.101 , pp. 2043-2052
    • Zhou, H.1    Skolnick, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.