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Volumn 46, Issue 3, 2006, Pages 1134-1142

The influence of variations of ligand protonation and tautomerism on protein-ligand recognition and binding energy landscape

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; COMPUTER SIMULATION; ENZYME KINETICS; PROTEINS; STRUCTURE (COMPOSITION);

EID: 33745401244     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci050071n     Document Type: Article
Times cited : (16)

References (34)
  • 4
    • 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, 470-489.
    • (1996) J. Mol. Biol. , vol.261 , pp. 470-489
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.4
  • 5
    • 0030154893 scopus 로고    scopus 로고
    • Hammerhead: Fast, fully flexible automated docking of flexible ligands to protein binding sites
    • Welch, W.; Ruppert, J.; Jain, A. N. Hammerhead: Fast, Fully Flexible Automated Docking of Flexible Ligands to Protein Binding Sites. Chem. Biol. 1996, 3, 449-462.
    • (1996) Chem. Biol. , vol.3 , pp. 449-462
    • Welch, W.1    Ruppert, J.2    Jain, A.N.3
  • 6
    • 0028854034 scopus 로고
    • Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation
    • Jones, G.; Willet, P.; Glen, R. C. Molecular Recognition of Receptor Sites Using a Genetic Algorithm with a Description of Desolvation. J. Mol. Biol. 1995, 245, 43-53.
    • (1995) J. Mol. Biol. , vol.245 , pp. 43-53
    • Jones, G.1    Willet, P.2    Glen, R.C.3
  • 7
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • Jones, G.; Willet, P.; Glen, R. C.; Leach, A. R.; Taylor, R. Development and Validation of a Genetic Algorithm for Flexible Docking. J. Mol. Biol. 1997, 267, 727-748.
    • (1997) J. Mol. Biol. , vol.267 , pp. 727-748
    • Jones, G.1    Willet, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
  • 8
    • 0032054612 scopus 로고    scopus 로고
    • Theory of biomolecular recognition
    • McCammon, J. A. Theory of Biomolecular Recognition. Curr. Opin. Struct. Biol. 1998, 8, 245-249.
    • (1998) Curr. Opin. Struct. Biol. , vol.8 , pp. 245-249
    • McCammon, J.A.1
  • 9
    • 0028410583 scopus 로고
    • Detailed ab initio prediction of lysozyme-antibody complex with 1.6 Å accuracy
    • Totrov, M.; Abagyan, R. Detailed ab initio Prediction of Lysozyme-Antibody Complex with 1.6 Å Accuracy. Nat. Struct. Biol. 1994, 1, 259-263.
    • (1994) Nat. Struct. Biol. , vol.1 , pp. 259-263
    • Totrov, M.1    Abagyan, R.2
  • 10
    • 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, 1035-1042.
    • (2001) J. Med. Chem. , vol.44 , pp. 1035-1042
    • Stahl, M.1    Rarey, M.2
  • 11
    • 0037763817 scopus 로고    scopus 로고
    • Comparative evaluation of 11 scoring functions for molecular docking
    • Wang, R.; Lu, Y.; Wang, S. Comparative Evaluation of 11 Scoring Functions for Molecular Docking. J. Med. Chem. 2003, 46, 2287-2303.
    • (2003) J. Med. Chem. , vol.46 , pp. 2287-2303
    • Wang, R.1    Lu, Y.2    Wang, S.3
  • 12
    • 0035829446 scopus 로고    scopus 로고
    • Evaluation of docking functions for protein-ligand docking
    • Pérez, C.; Ortiz, A. R. Evaluation of Docking Functions for Protein-Ligand Docking. J. Med. Chem. 2001, 44, 3768-3785.
    • (2001) J. Med. Chem. , vol.44 , pp. 3768-3785
    • Pérez, C.1    Ortiz, A.R.2
  • 15
    • 0024357911 scopus 로고
    • Formation of unique structure in polypeptide chains: Theoretical investigation with the aid of a replica approach
    • Shakhnovich, E.; Gutin, A. Formation of Unique Structure in Polypeptide Chains: Theoretical Investigation with the Aid of a Replica Approach. Biophys. Chem. 1989, 34, 187-199.
    • (1989) Biophys. Chem. , vol.34 , pp. 187-199
    • Shakhnovich, E.1    Gutin, A.2
  • 16
    • 0023449962 scopus 로고
    • Spin glasses and the statistical mechanics of protein folding
    • Bryngelson, J. D.; Wolynes, P. G. Spin Glasses and the Statistical Mechanics of Protein Folding. Proc. Natl. Acad. Sci. U.S.A. 1987, 84, 7524-7528.
    • (1987) Proc. Natl. Acad. Sci. U.S.A. , vol.84 , pp. 7524-7528
    • Bryngelson, J.D.1    Wolynes, P.G.2
  • 18
    • 0031465967 scopus 로고    scopus 로고
    • "New view" of protein folding reconciled with the old through multiple unfolding simulations
    • Lazaridis, T.; Karplus, M. "New View" of Protein Folding Reconciled with the Old Through Multiple Unfolding Simulations. Science 1997, 278, 1928-1931.
    • (1997) Science , vol.278 , pp. 1928-1931
    • Lazaridis, T.1    Karplus, M.2
  • 19
    • 0032842870 scopus 로고    scopus 로고
    • The fundamentals of protein folding: Bringing together theory and experiment
    • Dobson, C. M.; Karplus, K. The Fundamentals of Protein Folding: Bringing Together Theory and Experiment. Curr. Opin. Struct. Biol. 1999, 9, 92-101.
    • (1999) Curr. Opin. Struct. Biol. , vol.9 , pp. 92-101
    • Dobson, C.M.1    Karplus, K.2
  • 20
    • 0002006297 scopus 로고
    • Are there pathways for protein folding?
    • Levinthal, C. Are There Pathways for Protein Folding? J. Chem. Phys. 1968, 65, 44-45.
    • (1968) J. Chem. Phys. , vol.65 , pp. 44-45
    • Levinthal, C.1
  • 21
    • 0037058992 scopus 로고    scopus 로고
    • Probing the folding free energy landscape of the src-SH3 protein domain
    • Shea, J.-M.; Onuchic, J. N.; Brooks, C. L. Probing the Folding Free Energy Landscape of the src-SH3 Protein Domain. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 16064-16068.
    • (2002) Proc. Natl. Acad. Sci. U.S.A. , vol.99 , pp. 16064-16068
    • Shea, J.-M.1    Onuchic, J.N.2    Brooks, C.L.3
  • 23
    • 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
  • 24
    • 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
  • 25
    • 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.
    • (2003) Phys. Rev. Lett. , vol.90 , pp. 188101
    • Wang, J.1    Verkhivker, G.M.2
  • 26
    • 2942519283 scopus 로고    scopus 로고
    • Assessment of multiple binding modes in ligand-protein docking
    • Källblad, 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
    • Källblad, P.1    Mancera, R.L.2    Todorov, N.P.3
  • 28
    • 0032111471 scopus 로고    scopus 로고
    • A Branch-and-bound method for optimal atom-type assignment in de novo ligand design
    • Todorov, N. P.; Dean, P. M. A Branch-and-Bound Method for Optimal Atom-Type Assignment in de novo Ligand Design. J. Comput.-Aided Mol. Des. 1998, 12, 335-349.
    • (1998) J. Comput.-aided Mol. Des. , vol.12 , pp. 335-349
    • Todorov, N.P.1    Dean, P.M.2
  • 32
    • 0020441466 scopus 로고
    • Crystal structures of escherichia coli and lactobacillus casei dihydrofolate reductase refined at 1.7 å resolution, I. general features of binding of methtrexate
    • Bolin, J. T.; Filman, D. J.; Matthews, D. A.; Hamlin, R. C.; Kraut, J. Crystal Structures of Escherichia coli and Lactobacillus casei Dihydrofolate Reductase Refined at 1.7 Å Resolution, I. General Features of Binding of Methtrexate. J. Biol. Chem. 1982, 257, 13650-13562.
    • (1982) J. Biol. Chem. , vol.257 , pp. 13650-113562
    • Bolin, J.T.1    Filman, D.J.2    Matthews, D.A.3    Hamlin, R.C.4    Kraut, J.5
  • 33
    • 0028305456 scopus 로고
    • Refined structure of transketolase from saccaromyces cerevisiae at 2.0 å resolution
    • Nikkola, M.; Lindqvist, Y.; Schneider, G. Refined Structure of Transketolase from Saccaromyces cerevisiae at 2.0 Å Resolution. J. Mol. Biol. 1994, 238, 387-404.
    • (1994) J. Mol. Biol. , vol.238 , pp. 387-404
    • Nikkola, M.1    Lindqvist, Y.2    Schneider, G.3
  • 34
    • 0029032663 scopus 로고
    • Studies on crystal structures, active-centre geometry and denaturating mechanism of two ribosome inactivating proteins
    • Huang, Q.; Liu, S. Y.; Tang, Y.; Jin, S.; Wang, Y. Studies on Crystal Structures, Active-Centre Geometry and Denaturating Mechanism of Two Ribosome Inactivating Proteins. Biochem. J. 1995, 309, 285-298.
    • (1995) Biochem. J. , vol.309 , pp. 285-298
    • Huang, Q.1    Liu, S.Y.2    Tang, Y.3    Jin, S.4    Wang, Y.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.