Publications
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2011. Free energy profiles along consensus normal modes provide insight into HIV-1 protease flap opening. J. Chem. Theor. Comput.. 7:2348–52.
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2011. Free energy profiles along consensus normal modes provide insight into HIV-1 protease flap opening. J. Chem. Theor. Comput.. 7:2348–52.
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2011. Free energy profiles along consensus normal modes provide insight into HIV-1 protease flap opening. J. Chem. Theor. Comput.. 7:2348–52.
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2011. FvNano: A Virtual Laboratory to Manipulate Molecular Systems. 1st IEEE symposium on biological data visualization, Providence, RI @ ieee visweek, 2011, N# 136.
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2011. Impact of Thermostats on Folding and Aggregation Properties of Peptides Using the Optimized Potential for Efficient Structure Prediction Coarse-Grained Model. J. Chem. Theory Comput.. 7:1502–1510.
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2011. Optimizing the design of oligonucleotides for homology directed gene targeting. Plos One. 6:e14795.
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2011. Receptor Flexibility in Ligand Docking and Virtual Screening.. In-silico lead discovery.
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2010. Consensus Modes, a robust description of protein collective motions from multiple-minima normal mode analysis–application to the HIV-1 protease.. Phys. Chem. Chem. Phys.. 12:2850–2859.
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2010. Consensus Modes, a robust description of protein collective motions from multiple-minima normal mode analysis–application to the HIV-1 protease.. Phys. Chem. Chem. Phys.. 12:2850–2859.
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2010. How cations can assist DNase I in DNA binding and hydrolysis. Plos Comput. Biol.. 6:e1001000.
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2010. HiRE-RNA: A High Resolution Coarse-Grained Energy Model for RNA. J. Phys. Chem. B. 114:11957–11966.
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2010. How does heparin prevent the pH inactivation of cathepsin B? Allosteric mechanism elucidated by docking and molecular dynamics. Bmc Genomics. 11, S5
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2010. Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments. Nucleic Acids Res.. 38:6313–6323.
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2010. Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments. Nucleic Acids Res.. 38:6313–6323.
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2010. Nonequilibrium molecular dynamics simulation of the energy transport through a peptide helix. J. Chem. Phys.. 132
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2010. One-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue. Proc. Natl. Acad. Sci. U.s.a.. 107:6275–6280.
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2010. Protein-Protein Docking. Protein-Protein Complexes. Analysis, Modeling and Drug Design. :147–181.
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2010. Atomic structure and dynamics of pentameric ligand-gated ion channels: new insight from bacterial homologues. J. Physiol. (lond.). 588:565–572.
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2009. Deforming DNA: from physics to biology. Chemphyschem. 10:1399–404.
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2009. Mean field and the confined single homopolymer. Mol. Phys.. 107:1303–1312.
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2009. Mean field and the confined single homopolymer. Mol. Phys.. 107:1303–1312.
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2009. Molecular dynamics simulation of cooling: Heat transfer from a photoexcited peptide to the solvent. J. Chem. Phys.. 131
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2009. An optimized extended DNA kappa B site that enhances plasmid DNA nuclear import and gene expression. J. Gene Med.. 11:401–411.
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2009. Numerical studies of Lifshitz interactions between dielectrics. Phys. Rev. A. 79:020102(R).
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2009. PTools: an opensource molecular docking library.. Bmc Struct. Biol.. 9:27–37.