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Volumn 143, Issue 3, 2009, Pages 139-144

Continued development of an empirical function for predicting and rationalizing protein-protein binding affinities

Author keywords

Alanine scanning mutagenesis; Binding affinity; Biologics; Computational; Free energy; Hot spot; Peptide therapeutics; Protein protein recognition

Indexed keywords

ALANINE; AROMATIC COMPOUND; MUTANT PROTEIN;

EID: 67349178167     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2009.05.003     Document Type: Article
Times cited : (8)

References (20)
  • 1
    • 3142745414 scopus 로고    scopus 로고
    • Structural mining: self-consistent design on flexible protein-peptide docking and transferable binding affinity potential
    • Liu Z., Dominy B.N., and Shakhnovich E.I. Structural mining: self-consistent design on flexible protein-peptide docking and transferable binding affinity potential. J. Am. Chem. Soc. 126 27 (2004) 8515-8528
    • (2004) J. Am. Chem. Soc. , vol.126 , Issue.27 , pp. 8515-8528
    • Liu, Z.1    Dominy, B.N.2    Shakhnovich, E.I.3
  • 2
    • 23144436398 scopus 로고    scopus 로고
    • The FoldX web server: an online force field
    • (Web Server issue)
    • Schymkowitz J., et al. The FoldX web server: an online force field. Nucleic Acids Res. 33 (2005) W382-W388 (Web Server issue)
    • (2005) Nucleic Acids Res. , vol.33
    • Schymkowitz, J.1
  • 3
    • 17144383951 scopus 로고    scopus 로고
    • A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes
    • Zhang C., et al. A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes. J. Med. Chem. 48 7 (2005) 2325-2335
    • (2005) J. Med. Chem. , vol.48 , Issue.7 , pp. 2325-2335
    • Zhang, C.1
  • 4
    • 24344456625 scopus 로고    scopus 로고
    • Study of the insulin dimerization: binding free energy calculations and per-residue free energy decomposition
    • Zoete V., Meuwly M., and Karplus M. Study of the insulin dimerization: binding free energy calculations and per-residue free energy decomposition. Proteins 61 1 (2005) 79-93
    • (2005) Proteins , vol.61 , Issue.1 , pp. 79-93
    • Zoete, V.1    Meuwly, M.2    Karplus, M.3
  • 5
    • 57649140709 scopus 로고    scopus 로고
    • Novel therapeutic modalities to address nondrugable protein interaction targets
    • De Souza E.B., et al. Novel therapeutic modalities to address nondrugable protein interaction targets. Neuropsychopharmacology 34 1 (2009) 142-158
    • (2009) Neuropsychopharmacology , vol.34 , Issue.1 , pp. 142-158
    • De Souza, E.B.1
  • 6
    • 33746879536 scopus 로고    scopus 로고
    • Peptides and peptidomimetics in medicine, surgery and biotechnology
    • Gentilucci L., Tolomelli A., and Squassabia F. Peptides and peptidomimetics in medicine, surgery and biotechnology. Curr. Med. Chem. 13 20 (2006) 2449-2466
    • (2006) Curr. Med. Chem. , vol.13 , Issue.20 , pp. 2449-2466
    • Gentilucci, L.1    Tolomelli, A.2    Squassabia, F.3
  • 7
    • 54849425126 scopus 로고    scopus 로고
    • Discovering and improving novel peptide therapeutics
    • McGregor D.P. Discovering and improving novel peptide therapeutics. Curr. Opin. Pharmacol. 8 5 (2008) 616-619
    • (2008) Curr. Opin. Pharmacol. , vol.8 , Issue.5 , pp. 616-619
    • McGregor, D.P.1
  • 8
    • 3442901156 scopus 로고    scopus 로고
    • Small molecules for small minds? The case for biologic pharmaceuticals
    • Projan S.J., et al. Small molecules for small minds? The case for biologic pharmaceuticals. Expert Opin. Biol. Ther. 4 8 (2004) 1345-1350
    • (2004) Expert Opin. Biol. Ther. , vol.4 , Issue.8 , pp. 1345-1350
    • Projan, S.J.1
  • 9
    • 41049098705 scopus 로고    scopus 로고
    • Computer-aided, rational design of a potent and selective small peptide inhibitor of cyclooxygenase 2 (COX2)
    • Rajakrishnan V., Manoj V.R., and Subba Rao G. Computer-aided, rational design of a potent and selective small peptide inhibitor of cyclooxygenase 2 (COX2). J. Biomol. Struct. Dyn. 25 5 (2008) 535-542
    • (2008) J. Biomol. Struct. Dyn. , vol.25 , Issue.5 , pp. 535-542
    • Rajakrishnan, V.1    Manoj, V.R.2    Subba Rao, G.3
  • 10
    • 67349275522 scopus 로고    scopus 로고
    • Peptidic modulators of protein-protein interactions: progress and challenges in computational design
    • Rubinstein M., and Niv M.Y. Peptidic modulators of protein-protein interactions: progress and challenges in computational design. Biopolymers (2009)
    • (2009) Biopolymers
    • Rubinstein, M.1    Niv, M.Y.2
  • 11
    • 18144394737 scopus 로고    scopus 로고
    • Design and structure of peptide and peptidomimetic antagonists of protein-protein interaction
    • Sillerud L.O., and Larson R.S. Design and structure of peptide and peptidomimetic antagonists of protein-protein interaction. Curr. Protein Pept. Sci. 6 2 (2005) 151-169
    • (2005) Curr. Protein Pept. Sci. , vol.6 , Issue.2 , pp. 151-169
    • Sillerud, L.O.1    Larson, R.S.2
  • 12
    • 33846809046 scopus 로고    scopus 로고
    • In silico panning for a non-competitive peptide inhibitor
    • Yagi Y., et al. In silico panning for a non-competitive peptide inhibitor. BMC Bioinformatics 8 (2007) 11
    • (2007) BMC Bioinformatics , vol.8 , pp. 11
    • Yagi, Y.1
  • 13
    • 34547614501 scopus 로고    scopus 로고
    • A novel empirical free energy function that explains and predicts protein-protein binding affinities
    • Audie J., and Scarlata S. A novel empirical free energy function that explains and predicts protein-protein binding affinities. Biophys. Chemist. 129 2-3 (2007) 198-211
    • (2007) Biophys. Chemist. , vol.129 , Issue.2-3 , pp. 198-211
    • Audie, J.1    Scarlata, S.2
  • 14
    • 50549092426 scopus 로고    scopus 로고
    • Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions
    • Ritchie D.W., Kozakov D., and Vajda S. Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions. Bioinformatics 24 17 (2008) 1865-1873
    • (2008) Bioinformatics , vol.24 , Issue.17 , pp. 1865-1873
    • Ritchie, D.W.1    Kozakov, D.2    Vajda, S.3
  • 15
    • 57649176930 scopus 로고    scopus 로고
    • Development and validation of an empirical free energy function for calculating protein-protein binding free energy surfaces
    • Audie J. Development and validation of an empirical free energy function for calculating protein-protein binding free energy surfaces. Biophys. Chemist. 139 2-3 (2009) 84-91
    • (2009) Biophys. Chemist. , vol.139 , Issue.2-3 , pp. 84-91
    • Audie, J.1
  • 16
    • 0036291145 scopus 로고    scopus 로고
    • Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations
    • Guerois R., Nielsen J.E., and Serrano L. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J. Mol. Biol. 320 2 (2002) 369-387
    • (2002) J. Mol. Biol. , vol.320 , Issue.2 , pp. 369-387
    • Guerois, R.1    Nielsen, J.E.2    Serrano, L.3
  • 17
    • 0037195144 scopus 로고    scopus 로고
    • A simple physical model for binding energy hot spots in protein-protein complexes
    • Kortemme T., and Baker D. A simple physical model for binding energy hot spots in protein-protein complexes. Proc. Natl. Acad. Sci. U. S. A. 99 22 (2002) 14116-14121
    • (2002) Proc. Natl. Acad. Sci. U. S. A. , vol.99 , Issue.22 , pp. 14116-14121
    • Kortemme, T.1    Baker, D.2
  • 18
    • 33847650393 scopus 로고    scopus 로고
    • Computational alanine scanning mutagenesis-an improved methodological approach
    • Moreira I.S., Fernandes P.A., and Ramos M.J. Computational alanine scanning mutagenesis-an improved methodological approach. J. Comput. Chem. 28 3 (2007) 644-654
    • (2007) J. Comput. Chem. , vol.28 , Issue.3 , pp. 644-654
    • Moreira, I.S.1    Fernandes, P.A.2    Ramos, M.J.3
  • 19
    • 0032777649 scopus 로고    scopus 로고
    • Dissection of the protein G B1 domain binding site for human IgG Fc fragment
    • Sloan D.J., and Hellinga H.W. Dissection of the protein G B1 domain binding site for human IgG Fc fragment. Protein Sci. 8 8 (1999) 1643-1648
    • (1999) Protein Sci. , vol.8 , Issue.8 , pp. 1643-1648
    • Sloan, D.J.1    Hellinga, H.W.2
  • 20
    • 0035066602 scopus 로고    scopus 로고
    • ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions
    • Thorn K.S., and Bogan A.A. ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions. Bioinformatics 17 3 (2001) 284-285
    • (2001) Bioinformatics , vol.17 , Issue.3 , pp. 284-285
    • Thorn, K.S.1    Bogan, A.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.