메뉴 건너뛰기




Volumn 53, Issue 10, 2013, Pages 2559-2570

Computation of binding energies including their enthalpy and entropy components for protein-ligand complexes using support vector machines

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEXATION; COMPUTATIONAL METHODS; CORRELATION METHODS; ENTHALPY; ENTROPY; FORECASTING; LIGANDS; PROTEINS; SUPPORT VECTOR MACHINES;

EID: 84887106527     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci400321r     Document Type: Article
Times cited : (20)

References (51)
  • 1
    • 84859313336 scopus 로고    scopus 로고
    • Thermodynamic studies for drug design and screening
    • Garbett, N. C.; Chaires, J. B. Thermodynamic studies for drug design and screening Expert Opin. Drug Discovery 2012, 7, 299-314
    • (2012) Expert Opin. Drug Discovery , vol.7 , pp. 299-314
    • Garbett, N.C.1    Chaires, J.B.2
  • 2
    • 77957229353 scopus 로고    scopus 로고
    • Thermodynamics guided lead discovery and optimization
    • Ferenczy, G. G.; Keseru, G. M. Thermodynamics guided lead discovery and optimization Drug Discovery Today 2010, 15, 919-932
    • (2010) Drug Discovery Today , vol.15 , pp. 919-932
    • Ferenczy, G.G.1    Keseru, G.M.2
  • 3
    • 0032901515 scopus 로고    scopus 로고
    • Isothermal titration calorimetry and differential scanning calorimetry as complementary tools to investigate the energetics of biomolecular recognition
    • Jelesarov, I.; Bosshard, H. R. Isothermal titration calorimetry and differential scanning calorimetry as complementary tools to investigate the energetics of biomolecular recognition J. Mol. Recognit. 1999, 12, 3-18
    • (1999) J. Mol. Recognit. , vol.12 , pp. 3-18
    • Jelesarov, I.1    Bosshard, H.R.2
  • 4
    • 56549131177 scopus 로고    scopus 로고
    • The thermodynamics of protein-ligand interaction and solvation: Insights for ligand design
    • Olsson, T. S.; Williams, M. A.; Pitt, W. R.; Ladbury, J. E. The thermodynamics of protein-ligand interaction and solvation: insights for ligand design J. Mol. Biol. 2008, 384, 1002-1017
    • (2008) J. Mol. Biol. , vol.384 , pp. 1002-1017
    • Olsson, T.S.1    Williams, M.A.2    Pitt, W.R.3    Ladbury, J.E.4
  • 5
    • 80051775090 scopus 로고    scopus 로고
    • Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration
    • Genheden, S.; Mikulskis, P.; Hu, L.; Kongsted, J.; Soderhjelm, P.; Ryde, U. Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration J. Am. Chem. Soc. 2011, 133, 13081-13092
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 13081-13092
    • Genheden, S.1    Mikulskis, P.2    Hu, L.3    Kongsted, J.4    Soderhjelm, P.5    Ryde, U.6
  • 6
    • 84856776282 scopus 로고    scopus 로고
    • Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization
    • Beuming, T.; Che, Y.; Abel, R.; Kim, B.; Shanmugasundaram, V.; Sherman, W. Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization Proteins 2012, 80, 871-883
    • (2012) Proteins , vol.80 , pp. 871-883
    • Beuming, T.1    Che, Y.2    Abel, R.3    Kim, B.4    Shanmugasundaram, V.5    Sherman, W.6
  • 8
    • 0034618512 scopus 로고    scopus 로고
    • Entropy-enthalpy compensation and anticompensation: Solvation and ligand binding
    • Exner, O. Entropy-enthalpy compensation and anticompensation: solvation and ligand binding Chem. Commun. 2000, 1655-1656
    • (2000) Chem. Commun. , pp. 1655-1656
    • Exner, O.1
  • 9
    • 0001594721 scopus 로고    scopus 로고
    • Entropy-enthalpy compensation in solvation and ligand binding revisited
    • Gallicchio, E.; Kubo, M. M.; Levy, R. M. Entropy-enthalpy compensation in solvation and ligand binding revisited J. Am. Chem. Soc. 1998, 120, 4526-4527
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 4526-4527
    • Gallicchio, E.1    Kubo, M.M.2    Levy, R.M.3
  • 10
    • 33751157207 scopus 로고
    • Enthalpy-entropy compensation in drug-receptor binding
    • Gilli, P.; Ferretti, V.; Gilli, G.; Borea, P. A. Enthalpy-entropy compensation in drug-receptor binding J. Phys. Chem. 1994, 98, 1515-1518
    • (1994) J. Phys. Chem. , vol.98 , pp. 1515-1518
    • Gilli, P.1    Ferretti, V.2    Gilli, G.3    Borea, P.A.4
  • 11
    • 77954636329 scopus 로고    scopus 로고
    • Drug resistance in antiviral therapy
    • Locarnini, S.; Bowden, S. Drug resistance in antiviral therapy Clin. Liver Dis. 2010, 14, 439-459
    • (2010) Clin. Liver Dis. , vol.14 , pp. 439-459
    • Locarnini, S.1    Bowden, S.2
  • 13
    • 52049123291 scopus 로고    scopus 로고
    • Do enthalpy and entropy distinguish first in class from best in class?
    • Freire, E. Do enthalpy and entropy distinguish first in class from best in class? Drug Discovery Today 2008, 13, 869-874
    • (2008) Drug Discovery Today , vol.13 , pp. 869-874
    • Freire, E.1
  • 16
    • 0141990820 scopus 로고    scopus 로고
    • Specific empirical free energy function for automated docking of carbohydrates to proteins
    • Laederach, A.; Reilly, P. J. Specific empirical free energy function for automated docking of carbohydrates to proteins J. Comput. Chem. 2003, 24, 1748-1757
    • (2003) J. Comput. Chem. , vol.24 , pp. 1748-1757
    • Laederach, A.1    Reilly, P.J.2
  • 17
    • 0029995624 scopus 로고    scopus 로고
    • VALIDATE: A new method for the receptor-based prediction of binding affinities of novel ligands
    • 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
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 3959-3969
    • Head, R.D.1    Smythe, M.L.2    Oprea, T.I.3    Waller, C.L.4    Green, S.M.5    Marshall, G.R.6
  • 18
    • 0028106228 scopus 로고
    • Enthalpy-entropy compensation in the thermodynamics of hydrophobicity
    • discussion 277-278
    • Lee, B. Enthalpy-entropy compensation in the thermodynamics of hydrophobicity Biophys. Chem. 1994, 51, 271-277 discussion 277-278
    • (1994) Biophys. Chem. , vol.51 , pp. 271-277
    • Lee, B.1
  • 19
    • 84862768641 scopus 로고    scopus 로고
    • Decreasing the configurational entropy and the hydrophobicity of EBV-derived peptide 11389 increased its antigenicity, immunogenicity and its ability of inducing IL-6
    • Urquiza, M.; Guevara, T.; Rodriguez, C.; Melo-Cardenas, J.; Vanegas, M.; Patarroyo, M. E. Decreasing the configurational entropy and the hydrophobicity of EBV-derived peptide 11389 increased its antigenicity, immunogenicity and its ability of inducing IL-6 Amino Acids 2012, 42, 2165-2175
    • (2012) Amino Acids , vol.42 , pp. 2165-2175
    • Urquiza, M.1    Guevara, T.2    Rodriguez, C.3    Melo-Cardenas, J.4    Vanegas, M.5    Patarroyo, M.E.6
  • 20
    • 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
  • 21
    • 0031226772 scopus 로고    scopus 로고
    • Empirical scoring functions 0.1. 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 0.1. 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
  • 22
    • 84887037960 scopus 로고    scopus 로고
    • Semiempirical scoring functions for ligand binding based on molecular mechanics and continuum model calculations
    • Cheney, D. L.; Mason, J. S. Semiempirical scoring functions for ligand binding based on molecular mechanics and continuum model calculations Abstr. Pap. Am. Chem. Soc. 2000, 219, U600-U600
    • (2000) Abstr. Pap. Am. Chem. Soc. , vol.219
    • Cheney, D.L.1    Mason, J.S.2
  • 23
    • 0036022960 scopus 로고    scopus 로고
    • Further development and validation of empirical scoring functions for structure-based binding affinity prediction
    • Wang, R. X.; Lai, L. H.; Wang, S. M. 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.X.1    Lai, L.H.2    Wang, S.M.3
  • 24
    • 84887089575 scopus 로고    scopus 로고
    • Comparative evaluation of five scoring functions for accurate prediction of protein-ligand binding energy
    • Puvanendrampillai, D.; Marsden, P. M.; Mitchell, J. B. O.; Glen, R. C. Comparative evaluation of five scoring functions for accurate prediction of protein-ligand binding energy Abstr. Pap. Am. Chem. Soc. 2004, 227, U1018-U1018
    • (2004) Abstr. Pap. Am. Chem. Soc. , vol.227
    • Puvanendrampillai, D.1    Marsden, P.M.2    Mitchell, J.B.O.3    Glen, R.C.4
  • 25
    • 84887081622 scopus 로고    scopus 로고
    • Novel scoring functions for in silico database screening: Binding response and pose-based scaling
    • Zhong, S. J.; MacKerell, A. D. Novel scoring functions for in silico database screening: Binding response and pose-based scaling Abstr. Pap. Am. Chem. Soc. 2005, 230, U1307-U1307
    • (2005) Abstr. Pap. Am. Chem. Soc. , vol.230
    • Zhong, S.J.1    MacKerell, A.D.2
  • 26
    • 80053302991 scopus 로고    scopus 로고
    • Evaluation of several two-step scoring functions based on linear interaction energy, effective ligand size, and empirical pair potentials for prediction of protein-ligand binding geometry and free energy
    • Rahaman, O.; Estrada, T. P.; Doren, D. J.; Taufer, M.; Brooks, C. L.; Armen, R. S. Evaluation of several two-step scoring functions based on linear interaction energy, effective ligand size, and empirical pair potentials for prediction of protein-ligand binding geometry and free energy J. Chem. Inf. Model. 2011, 51, 2047-2065
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 2047-2065
    • Rahaman, O.1    Estrada, T.P.2    Doren, D.J.3    Taufer, M.4    Brooks, C.L.5    Armen, R.S.6
  • 27
    • 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. Inclusion of solvation and entropy in the knowledge-based scoring function for protein-ligand interactions J. Chem. Inf. Model. 2010, 50, 262-273
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 262-273
    • Huang, S.Y.1    Zou, X.2
  • 28
    • 84887040498 scopus 로고    scopus 로고
    • What is the statistical-thermodynamic cost of binding entropy in protein-ligand docking and virtual screening? Analysis based on the use of 11 scoring functions
    • Ruvinsky, A. M. What is the statistical-thermodynamic cost of binding entropy in protein-ligand docking and virtual screening? Analysis based on the use of 11 scoring functions J. Biomol. Struct. Dyn. 2007, 24, 767-768
    • (2007) J. Biomol. Struct. Dyn. , vol.24 , pp. 767-768
    • Ruvinsky, A.M.1
  • 29
    • 79952148691 scopus 로고    scopus 로고
    • PHOENIX: A scoring function for affinity prediction derived using high-resolution crystal structures and calorimetry measurements
    • Tang, Y. T.; Marshall, G. R. PHOENIX: A scoring function for affinity prediction derived using high-resolution crystal structures and calorimetry measurements J. Chem. Inf. Model. 2011, 51, 214-228
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 214-228
    • Tang, Y.T.1    Marshall, G.R.2
  • 30
    • 34249753618 scopus 로고
    • Support-vector networks
    • Cortes, C.; Vapnik, V. Support-vector networks Mach. Learn. 1995, 20, 273-297
    • (1995) Mach. Learn. , vol.20 , pp. 273-297
    • Cortes, C.1    Vapnik, V.2
  • 31
    • 0036086337 scopus 로고    scopus 로고
    • Support vector machines with selective kernel scaling for protein classification and identification of key amino acid positions
    • Zavaljevski, N.; Stevens, F. J.; Reifman, J. Support vector machines with selective kernel scaling for protein classification and identification of key amino acid positions Bioinformatics 2002, 18, 689-696
    • (2002) Bioinformatics , vol.18 , pp. 689-696
    • Zavaljevski, N.1    Stevens, F.J.2    Reifman, J.3
  • 32
    • 0037423777 scopus 로고    scopus 로고
    • Support vector machines for prediction of protein domain structural class
    • Cai, Y. D.; Liu, X. J.; Xu, X. B.; Chou, K. C. Support vector machines for prediction of protein domain structural class J. Theor. Biol. 2003, 221, 115-120
    • (2003) J. Theor. Biol. , vol.221 , pp. 115-120
    • Cai, Y.D.1    Liu, X.J.2    Xu, X.B.3    Chou, K.C.4
  • 33
    • 0038644483 scopus 로고    scopus 로고
    • Support vector machines for predicting rRNA-, RNA-, and DNA-binding proteins from amino acid sequence
    • Cai, Y. D.; Lin, S. L. Support vector machines for predicting rRNA-, RNA-, and DNA-binding proteins from amino acid sequence Biochim. Biophys. Acta 2003, 1648, 127-133
    • (2003) Biochim. Biophys. Acta , vol.1648 , pp. 127-133
    • Cai, Y.D.1    Lin, S.L.2
  • 34
    • 12244271454 scopus 로고    scopus 로고
    • Predicting CNS permeability of drug molecules: Comparison of neural network and support vector machine algorithms
    • Doniger, S.; Hofmann, T.; Yeh, J. Predicting CNS permeability of drug molecules: Comparison of neural network and support vector machine algorithms J. Comput. Biol. 2002, 9, 849-864
    • (2002) J. Comput. Biol. , vol.9 , pp. 849-864
    • Doniger, S.1    Hofmann, T.2    Yeh, J.3
  • 35
    • 0034740222 scopus 로고    scopus 로고
    • Drug design by machine learning: Support vector machines for pharmaceutical data analysis
    • Burbidge, R.; Trotter, M.; Buxton, B.; Holden, S. Drug design by machine learning: Support vector machines for pharmaceutical data analysis Comput. Chem. 2001, 26, 5-14
    • (2001) Comput. Chem. , vol.26 , pp. 5-14
    • Burbidge, R.1    Trotter, M.2    Buxton, B.3    Holden, S.4
  • 36
    • 0035023445 scopus 로고    scopus 로고
    • Predicting protein-protein interactions from primary structure
    • Bock, J. R.; Gough, D. A. Predicting protein-protein interactions from primary structure Bioinformatics 2001, 17, 455-460
    • (2001) Bioinformatics , vol.17 , pp. 455-460
    • Bock, J.R.1    Gough, D.A.2
  • 37
    • 79952178127 scopus 로고    scopus 로고
    • A machine learning-based method to improve docking scoring functions and its application to drug repurposing
    • Kinnings, S. L.; Liu, N. N.; Tonge, P. J.; Jackson, R. M.; Xie, L.; Bourne, P. E. A machine learning-based method to improve docking scoring functions and its application to drug repurposing J. Chem. Inf. Model. 2011, 51, 408-419
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 408-419
    • Kinnings, S.L.1    Liu, N.N.2    Tonge, P.J.3    Jackson, R.M.4    Xie, L.5    Bourne, P.E.6
  • 38
    • 80053313926 scopus 로고    scopus 로고
    • Support vector regression scoring of receptor-ligand complexes for rank-ordering and virtual screening of chemical libraries
    • Li, L.; Wang, B.; Meroueh, S. O. Support vector regression scoring of receptor-ligand complexes for rank-ordering and virtual screening of chemical libraries J. Chem. Inf. Model. 2011, 51, 2132-2138
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 2132-2138
    • Li, L.1    Wang, B.2    Meroueh, S.O.3
  • 39
    • 79955401050 scopus 로고    scopus 로고
    • Target-specific support vector machine scoring in structure-based virtual screening: Computational validation, in vitro testing in kinases, and effects on lung cancer cell proliferation
    • Li, L. W.; Khanna, M.; Jo, I. H.; Wang, F.; Ashpole, N. M.; Hudmon, A.; Meroueh, S. O. Target-specific support vector machine scoring in structure-based virtual screening: Computational validation, in vitro testing in kinases, and effects on lung cancer cell proliferation J. Chem. Inf. Model. 2011, 51, 755-759
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 755-759
    • Li, L.W.1    Khanna, M.2    Jo, I.H.3    Wang, F.4    Ashpole, N.M.5    Hudmon, A.6    Meroueh, S.O.7
  • 40
    • 66249104367 scopus 로고    scopus 로고
    • Structure-based drug screening and ligand-based drug screening with machine learning
    • Fukunishi, Y. Structure-based drug screening and ligand-based drug screening with machine learning Comb. Chem. High Throughput Screening 2009, 12, 397-408
    • (2009) Comb. Chem. High Throughput Screening , vol.12 , pp. 397-408
    • Fukunishi, Y.1
  • 41
    • 65749110436 scopus 로고    scopus 로고
    • Computational intelligence methods for docking scores
    • Hecht, D.; Fogel, G. B. Computational intelligence methods for docking scores Curr. Comput.-Aided Drug Des. 2009, 5, 56-68
    • (2009) Curr. Comput.-Aided Drug Des. , vol.5 , pp. 56-68
    • Hecht, D.1    Fogel, G.B.2
  • 42
    • 0042034151 scopus 로고    scopus 로고
    • A new method to estimate ligand-receptor energetics
    • Bock, J. R.; Gough, D. A. A new method to estimate ligand-receptor energetics Mol. Cell. Proteomics 2002, 1, 904-910
    • (2002) Mol. Cell. Proteomics , vol.1 , pp. 904-910
    • Bock, J.R.1    Gough, D.A.2
  • 43
    • 43949128085 scopus 로고    scopus 로고
    • PDBcal: A comprehensive dataset for receptor-ligand interactions with three-dimensional structures and binding thermodynamics from isothermal titration calorimetry
    • Li, L. W.; Dantzer, J. J.; Nowacki, J.; O'Callaghan, B. J.; Meroueh, S. O. PDBcal: A comprehensive dataset for receptor-ligand interactions with three-dimensional structures and binding thermodynamics from isothermal titration calorimetry Chem. Biol. Drug Des. 2008, 71, 529-532
    • (2008) Chem. Biol. Drug Des. , vol.71 , pp. 529-532
    • Li, L.W.1    Dantzer, J.J.2    Nowacki, J.3    O'Callaghan, B.J.4    Meroueh, S.O.5
  • 44
  • 47
    • 0003120218 scopus 로고    scopus 로고
    • Fast training of support vector machines using sequential minimal optimization
    • MIT Press: Cambridge, MA, U.S.A.
    • Platt, J. C. Fast training of support vector machines using sequential minimal optimization In Advances in Kernel Methods; MIT Press: Cambridge, MA, U.S.A., 1999; pp 185-208.
    • (1999) Advances in Kernel Methods , pp. 185-208
    • Platt, J.C.1
  • 49
    • 10044294023 scopus 로고    scopus 로고
    • An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes
    • Wang, R. X.; Lu, Y. P.; Fang, X. L.; Wang, S. M. An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes J. Chem. Inf. Comput. Sci. 2004, 44, 2114-2125
    • (2004) J. Chem. Inf. Comput. Sci. , vol.44 , pp. 2114-2125
    • Wang, R.X.1    Lu, Y.P.2    Fang, X.L.3    Wang, S.M.4
  • 50
    • 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, 2287-2303
    • (2003) J. Med. Chem. , vol.46 , pp. 2287-2303
    • Wang, R.X.1    Lu, Y.P.2    Wang, S.M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.