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Volumn 18, Issue 3, 2012, Pages 1097-1106

Improving the desolvation penalty in empirical protein pK a modeling

Author keywords

Desolvation; PK a; PROPKA; Protein modeling; Solvation

Indexed keywords

CYCLIC AMP DEPENDENT PROTEIN KINASE; SOLVENT;

EID: 84861332261     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-011-1141-1     Document Type: Article
Times cited : (7)

References (20)
  • 1
    • 0019889036 scopus 로고
    • Calculations of enzymatic-reactions - Calculations of pKa, proton-transfer reactions, and general acid catalysis reactions in enzymes
    • Warshel A (1981) Calculations of enzymatic-reactions - calculations of pKa, proton-transfer reactions, and general acid catalysis reactions in enzymes. Biochemistry 20:3167-3177
    • (1981) Biochemistry , vol.20 , pp. 3167-3177
    • Warshel, A.1
  • 2
    • 79951476387 scopus 로고    scopus 로고
    • PROPKA3: Consistent treatment of internal and surface residues in empirical pKa predictions
    • Olsson MHM, Søndergaard CR, Rostkowski M, Jensen JH (2011) PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions. J Chem Theor Comput 2:525-537
    • (2011) J Chem Theor Comput , vol.2 , pp. 525-537
    • Olsson, M.H.M.1    Søndergaard, C.R.2    Rostkowski, M.3    Jensen, J.H.4
  • 3
    • 0015222647 scopus 로고
    • Interpretation of protein structures - Estimation of static accessibility
    • Lee B, Richards FM (1971) Interpretation of protein structures - estimation of static accessibility. J Mol Biol 55:379
    • (1971) J Mol Biol , vol.55 , pp. 379
    • Lee, B.1    Richards, F.M.2
  • 4
    • 34250928962 scopus 로고
    • Volumes and hydration warmth of ions
    • Born M (1920) Volumes and hydration warmth of ions. Z Phys 1:45-48
    • (1920) Z Phys , vol.1 , pp. 45-48
    • Born, M.1
  • 5
    • 0015520587 scopus 로고
    • Interpretation of protein titration curves - Application to lysozyme
    • Tanford C, Roxby R (1972) Interpretation of protein titration curves - application to lysozyme. Biochemistry 11:2192
    • (1972) Biochemistry , vol.11 , pp. 2192
    • Tanford, C.1    Roxby, R.2
  • 7
    • 11744256643 scopus 로고
    • Molecular interactions in solution: An overview of methods based on continuous distributions of the solvent
    • Tomasi J, Persico M (1994) Molecular interactions in solution - an overview of methods based on continuous distributions of the solvent. Chem Rev 94:2027-2094 (Pubitemid 124000195)
    • (1994) Chemical Reviews , vol.94 , Issue.7 , pp. 2027-2094
    • Tomasi, J.1    Persico, M.2
  • 8
    • 84961981091 scopus 로고    scopus 로고
    • Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics
    • Cramer CJ, Truhlar DG (1999) Implicit solvation models: equilibria, structure, spectra, and dynamics. Chem Rev 99:2161-2200 (Pubitemid 129585183)
    • (1999) Chemical Reviews , vol.99 , Issue.8 , pp. 2161-2200
    • Cramer, C.J.1    Truhlar, D.G.2
  • 9
    • 0025260385 scopus 로고
    • Excluded volume approximation to protein-solvent interaction. The solvent contact model
    • Colonnacesari F, Sander C (1990) Excluded volume approximation to protein-solvent interaction - the solvent contact model. Biophys J 57:1103-1107 (Pubitemid 20134205)
    • (1990) Biophysical Journal , vol.57 , Issue.5 , pp. 1103-1107
    • Colonna-Cesari, F.1    Sander, C.2
  • 12
    • 0025661993 scopus 로고
    • A precise analytical method for calculating the electrostatic energy of macromolecules in aqueoussolution
    • Schaefer M, Froemmel C (1990) A precise analytical method for calculating the electrostatic energy of macromolecules in aqueoussolution. J Mol Biol 216:1045-1066
    • (1990) J Mol Biol , vol.216 , pp. 1045-1066
    • Schaefer, M.1    Froemmel, C.2
  • 13
    • 0026110673 scopus 로고
    • The inclusion of electrostatic hydration energies in molecular mechanics calculations
    • Gilson MK, Honig B (1991) The inclusion of electrostatic hydration energies in molecular mechanics calculations. J Comput Aided Mol Des 5:5-20
    • (1991) J Comput Aided Mol des , vol.5 , pp. 5-20
    • Gilson, M.K.1    Honig, B.2
  • 14
    • 0012227656 scopus 로고    scopus 로고
    • A comprehensive analytical treatment of continuum electrostatics
    • Schaefer M, KarplusM(1996) A comprehensive analytical treatment of continuum electrostatics. J Phys Chem 100:1578-1599 (Pubitemid 126789971)
    • (1996) Journal of Physical Chemistry , vol.100 , Issue.5 , pp. 1578-1599
    • Schaefer, M.1    Karplus, M.2
  • 16
    • 0344778061 scopus 로고
    • Semianalytical treatment of solvation for molecular mechanics and dynamics
    • Still WC, Tempczyk A, Hawley RC, Hendrickson T (1990) Semianalytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc 112:6127-6129
    • (1990) J Am Chem Soc , vol.112 , pp. 6127-6129
    • Still, W.C.1    Tempczyk, A.2    Hawley, R.C.3    Hendrickson, T.4
  • 17
    • 0035451052 scopus 로고    scopus 로고
    • What are the dielectric "constants" of proteins and how to validate electrostatic models?
    • DOI 10.1002/prot.1106
    • Schutz CN, Warshel A (2001) What are the dielectric "constants" of proteins and how to validate electrostatic models? Proteins 44:400-417 (Pubitemid 32768578)
    • (2001) Proteins: Structure, Function and Genetics , vol.44 , Issue.4 , pp. 400-417
    • Schutz, C.N.1    Warshel, A.2
  • 18
    • 0026612756 scopus 로고
    • Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin
    • Bashford D, Gerwert K (1992) Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin. J Mol Biol 224:473-486
    • (1992) J Mol Biol , vol.224 , pp. 473-486
    • Bashford, D.1    Gerwert, K.2
  • 19
    • 0033135638 scopus 로고    scopus 로고
    • Effective energy function for proteins in solution
    • DOI 10.1002/(SICI)1097-0134(19990501)35:2<133::AID-PROT1>3.0.CO;2-N
    • Lazaridis T, Karplus M (1999) Effective energy function for proteins in solution. Protein Struct Funct Genet 35:133-152 (Pubitemid 29165128)
    • (1999) Proteins: Structure, Function and Genetics , vol.35 , Issue.2 , pp. 133-152
    • Lazaridis, T.1    Karplus, M.2
  • 20
    • 10044267947 scopus 로고    scopus 로고
    • Stabilization of internal charges in a protein: Water penetration or conformational change?
    • DOI 10.1529/biophysj.104.048454
    • Denisov VP, Schlessman JL, Garcia-Moreno B, Halle B (2004) Stabilization of internal charges in a protein: water penetration or conformational change? Biophys J 87:3982-3994 (Pubitemid 39602903)
    • (2004) Biophysical Journal , vol.87 , Issue.6 , pp. 3982-3994
    • Denisov, V.P.1    Schlessman, J.L.2    Garcia-Moreno, E.B.3    Halle, B.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.