메뉴 건너뛰기




Volumn 6, Issue 4, 2007, Pages 923-936

Electrostatic potential calculation for biomolecules - Creating a database of pre-calculated values reported on a per residue basis for all PDB protein structures

Author keywords

DelPhi; Electrostatic potential of biomolecules; Protein structure analysis; STING

Indexed keywords

AMINO ACID; LYSOZYME;

EID: 37349108548     PISSN: None     EISSN: 16765680     Source Type: Journal    
DOI: None     Document Type: Conference Paper
Times cited : (5)

References (21)
  • 2
    • 0021107965 scopus 로고
    • Solvent-accessible surfaces of proteins and nucleic acids
    • Connolly ML (1983). Solvent-accessible surfaces of proteins and nucleic acids. Science 221: 709-713.
    • (1983) Science , vol.221 , pp. 709-713
    • Connolly, M.L.1
  • 3
    • 84961981091 scopus 로고    scopus 로고
    • Implicit solvation models: Equilibria, structure, spectra, and dynamics
    • Cramer CJ and Truhlar DG (1999). Implicit solvation models: equilibria, structure, spectra, and dynamics. Chem. Ver. 99: 2161-2200.
    • (1999) Chem. Ver , vol.99 , pp. 2161-2200
    • Cramer, C.J.1    Truhlar, D.G.2
  • 4
    • 84986483798 scopus 로고
    • The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies
    • Eisenhaber F, Lijnzaad P, Argos P, Sander C, et al. (1995). The double cubic lattice method: efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies. J. Comput. Chem. 16: 273-285.
    • (1995) J. Comput. Chem , vol.16 , pp. 273-285
    • Eisenhaber, F.1    Lijnzaad, P.2    Argos, P.3    Sander, C.4
  • 5
    • 33749046258 scopus 로고    scopus 로고
    • Building multiple sequence alignments with a flavor of HSSP alignments
    • Higa RH, Cruz SA, Kuser PR, Yamagishi ME, et al. (2006). Building multiple sequence alignments with a flavor of HSSP alignments. Genet. Mol. Res. 5: 127-137.
    • (2006) Genet. Mol. Res , vol.5 , pp. 127-137
    • Higa, R.H.1    Cruz, S.A.2    Kuser, P.R.3    Yamagishi, M.E.4
  • 6
    • 0000486193 scopus 로고    scopus 로고
    • Adaptive multilevel finite element solution of the Poisson-Boltzmann equation I: Algorithm and examples
    • Holst M, Baker N and Wang M (2000). Adaptive multilevel finite element solution of the Poisson-Boltzmann equation I: Algorithm and examples. J. Comput. Chem. 21: 1319-1342.
    • (2000) J. Comput. Chem , vol.21 , pp. 1319-1342
    • Holst, M.1    Baker, N.2    Wang, M.3
  • 7
    • 0029016182 scopus 로고
    • Classical electrostatics in biology and chemistry
    • Honig B and Nicholls A (1995). Classical electrostatics in biology and chemistry. Science 268: 1144-1149.
    • (1995) Science , vol.268 , pp. 1144-1149
    • Honig, B.1    Nicholls, A.2
  • 8
    • 0042532200 scopus 로고    scopus 로고
    • STING Millennium: A web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence
    • Neshich G, Togawa RC, Mancini AL, Kuser PR, et al. (2003). STING Millennium: a web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence. Nucleic Acids Res. 31: 3386-3392.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3386-3392
    • Neshich, G.1    Togawa, R.C.2    Mancini, A.L.3    Kuser, P.R.4
  • 9
    • 3242878795 scopus 로고    scopus 로고
    • JavaProtein Dossier: A novel web-based data visualization tool for comprehensive analysis of protein structure
    • Neshich G, Rocchia W, Mancini AL, Yamagishi ME, et al. (2004). JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure. Nucleic Acids Res. 32: W595-W601.
    • (2004) Nucleic Acids Res , vol.32
    • Neshich, G.1    Rocchia, W.2    Mancini, A.L.3    Yamagishi, M.E.4
  • 11
    • 13444250000 scopus 로고    scopus 로고
    • STING Report: Convenient web-based application for graphic and tabular presentations of protein sequence, structure and function descriptors from the STING database
    • Neshich G, Mancini AL, Yamagishi ME, Kuser PR, et al. (2005b). STING Report: convenient web-based application for graphic and tabular presentations of protein sequence, structure and function descriptors from the STING database. Nucleic Acids Res. 33: D269-D274.
    • (2005) Nucleic Acids Res , vol.33
    • Neshich, G.1    Mancini, A.L.2    Yamagishi, M.E.3    Kuser, P.R.4
  • 12
    • 33845421969 scopus 로고    scopus 로고
    • The Star STING server: A multiplatform environment for protein structure analysis
    • Neshich G, Mazoni I, Oliveira SR, Yamagishi ME, et al. (2006). The Star STING server: a multiplatform environment for protein structure analysis. Genet. Mol. Res. 5: 717-722.
    • (2006) Genet. Mol. Res , vol.5 , pp. 717-722
    • Neshich, G.1    Mazoni, I.2    Oliveira, S.R.3    Yamagishi, M.E.4
  • 13
    • 0026319199 scopus 로고
    • Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons
    • Nicholls A, Sharp KA and Honig B (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    Sharp, K.A.2    Honig, B.3
  • 14
    • 0030828982 scopus 로고    scopus 로고
    • Electrostatic influence on the kinetics of ligand binding to acetylcholinesterase. Distinctions between active center ligands and fasciculin
    • Radic Z, Kirchhoff PD, Quinn DM, McCammon JA, et al. (1997). Electrostatic influence on the kinetics of ligand binding to acetylcholinesterase. Distinctions between active center ligands and fasciculin. J. Biol. Chem. 272: 23265-23277.
    • (1997) J. Biol. Chem , vol.272 , pp. 23265-23277
    • Radic, Z.1    Kirchhoff, P.D.2    Quinn, D.M.3    McCammon, J.A.4
  • 15
    • 0017429069 scopus 로고
    • Areas, volumes, packing and protein structure
    • Richards FM (1977). Areas, volumes, packing and protein structure. Annu. Rev. Biophys. Bioeng. 6: 151-176.
    • (1977) Annu. Rev. Biophys. Bioeng , vol.6 , pp. 151-176
    • Richards, F.M.1
  • 16
    • 26844507399 scopus 로고    scopus 로고
    • Poisson-Boltzmann equation boundary conditions for biological applications
    • Rocchia W (2005). Poisson-Boltzmann equation boundary conditions for biological applications. Math. Comput. Model. 41: 1109-1118.
    • (2005) Math. Comput. Model , vol.41 , pp. 1109-1118
    • Rocchia, W.1
  • 17
    • 0035913537 scopus 로고    scopus 로고
    • Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions
    • Rocchia W, Alexov E and Honig B (2001). Extending the applicability of the nonlinear Poisson-Boltzmann equation: multiple dielectric constants and multivalent ions. J. Phys. Chem. B. 105: 6507-6514.
    • (2001) J. Phys. Chem. B , vol.105 , pp. 6507-6514
    • Rocchia, W.1    Alexov, E.2    Honig, B.3
  • 18
    • 0037080244 scopus 로고    scopus 로고
    • Rapid grid-based construction of the molecular surface for both molecules and geometric objects: Applications to the finite difference Poisson-Boltzmann method
    • Rocchia W, Sridharan S, Nicholls A, Alexov E, et al. (2002). Rapid grid-based construction of the molecular surface for both molecules and geometric objects: applications to the finite difference Poisson-Boltzmann method. J. Comput. Chem. 23: 128-137.
    • (2002) J. Comput. Chem , vol.23 , pp. 128-137
    • Rocchia, W.1    Sridharan, S.2    Nicholls, A.3    Alexov, E.4
  • 19
  • 20
    • 0036923836 scopus 로고    scopus 로고
    • Differences in electrostatic properties at antibody-antigen binding sites: Implications for specificity and cross-reactivity
    • Sinha N, Mohan S, Lipschultz CA and Smith-Gill SJ (2002). Differences in electrostatic properties at antibody-antigen binding sites: implications for specificity and cross-reactivity. Biophys. J. 83: 2946-2968.
    • (2002) Biophys. J , vol.83 , pp. 2946-2968
    • Sinha, N.1    Mohan, S.2    Lipschultz, C.A.3    Smith-Gill, S.J.4
  • 21
    • 0033614004 scopus 로고
    • Word JM, Lovell SC, Richardson JS and Richardson DC (1999). Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation
    • Word JM, Lovell SC, Richardson JS and Richardson DC (1999). Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J. Mol. Biol. 285: 1735-1747.
    • (1735) J. Mol. Biol , vol.285


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.