References
- Verkhivker , G.M. 2004 . Computational analysis of ligand binding dynamics at the intermolecular hot spots with the aid of simulated tempering and binding free energy calculations . J. Mol. Graph. Model. , 22 : 335
- Marrone , T.J. , Briggs , J.M. and McCammon , J.A. 1997 . Structure-based drug design . Annu. Rev. Pharmacol. Toxicol. , 37 : 71
- Mirny , L.A. and Shakhnovich , E.I. 1999 . Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function . J. Mol. Biol. , 291 : 177
- Ding , F. , Dokholyan , N.V. , Buldyrev , S.V. , Stanley , H.E. and Shakhnovich , E.I. 2002 . Formation of the folding nucleus of an SH3 domain investigated by loosely coupled molecular dynamics . Biophys. J. , : 83
- Broglia , R.A. , Tiana , G. and Berera , R. 2003 . Resistance proof, folding-inhibitor drugs . J. Chem. Phys. , 118 : 4754
- Broglia , R.A. , Tiana , G. , Sutto , L. , Provasi , D. and Simona , F. Design of HIV-1-PR inhibitors which do not create resistance: blocking the folding of single monomers . Protein Sci. , (in press) (q-bio/0504011)
- Tiana , G. , Broglia , R.A. , Roman , H.E. , Vigezzi , E. and Shakhnovich , E. 1998 . Folding and misfolding of designed protein-like folding and misfolding of designed protein-like chains with mutations . J. Chem. Phys. , 108 : 757
- Broglia , R.A. , Tiana , G. and Provasi , D. 2004 . Simple model of protein folding and of non-conventional drug design . J. Phys. Cond. Matt. , 16 : R111
- Broglia , R.A. and Tiana , G. 2001 . Hierarchy of events in the folding of model proteins . J. Chem. Phys. , 114 : 7267
- Tiana , G. and Broglia , R.A. 2001 . Statistical analysis of native contact formation in the folding of designed model proteins . J. Chem. Phys. , 114 : 2503
- Go , N. 1983 . Theoretical studies of protein folding . Annu. Rev. Biophys. Bioengin. , 12 : 183
- Berendsen , H.J.C. , van der Spoel , D. and van Drunen , R. 1995 . GROMACS: A message-passing parallel molecular dynamics implementation . Comp. Phys. Comm. , 91 : 43
- Tiana , G. , Simona , F. , De Mori , G.M.S. , Broglia , R.A. and Colombo , G. 2004 . Understanding the determinants of stability and folding of small globular proteins from their energetics . Protein Sci. , 13 : 113
- Tomasselli , A.G. and Heinrikson , R.L. 2000 . Targetting the HIV-protease in AIDS therapy: a current clinical perspective . Biochem. Biophys. Acta , 1477 : 189
- Xie , D. , Gulnik , S. , Gustchina , E. , Yu , B. , Shao , W. , Qoronfleh , W. , Nathan , A. and Erickson , J.W. 1999 . Drug resistance mutations can effect dimer stability of HIV-1 protease at neutral pH . Protein Sci. , 8 : 1702
- Metha , M.L. 1990 . Random Matrices , San Diego : Academic Press .
- Shafer , R.W. , Hsu , P. , Patick , A.K. , Craig , C. and Brendel , V. 1999 . Identification of biased amino acid substitution patterns in human immunodeficiency virus type 1 . J. Virol. , 73 : 6197
- Bahar , I. , Atilgan , A.R. , Demirel , M.C. and Erman , B. 1998 . Vibrational dynamics of folded proteins: significance of slow and fast motions in relation to function and stability . Phys. Rev. Lett. , 80 : 2733
- Cecconi , F. , Micheletti , C. , Carloni , P. and Maritan , A. 2001 . Molecular dynamics studies on HIV-1 protease: drug resistance and folding pathways . Proteins , 43 : 365
- Levy , Y. , Caflisch , A. , Onuchic , J.N. and Wolynes , P.G. 2004 . The folding and dimerization of HIV-1 protease: evidence for a stable monomer from simulations . J. Mol. Biol. , 340 : 67
- Borg , J. 2001 . Optimized Monte Carlo analysis for generalized ensembles . Eur. Phys. J. B , 29 : 481
- Kaya , H. and Chan , H.S. 2000 . Polymer principles of calorimetric two-state cooperativity . Proteins , 40 : 637
- Li , M.S. , Klimov , D.K. and Thirumalai , D. 2004 . Finite-size effects on calorimetric operativity of two-state proteins q-bio/0412008