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. 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. Agonist trapped in ATP-binding sites of the P2X2 receptor. Proc. Natl. Acad. Sci. U.s.a.. 108:9066–9071.
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2011. GPU-accelerated atom and dynamic bond visualization using HyperBalls: a unified algorithm for balls, sticks and hyperboloids. J. Comput. Chem.. 32:2924–2935.
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2011. GPU-powered tools boost molecular visualization. Briefings Bioinf.. 12:689–701.
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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. Intrinsic Determinants of A beta(12-24) pH-Dependent Self-Assembly Revealed by Combined Computational and Experimental Studies. Plos One. 6:e24329.
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2011. Local elasticity of strained DNA studied by all-atom simulations. Phys. Rev. E. 84:021903.
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2011. A Multiscale Approach to Characterize the Early Aggregation Steps of the Amyloid-Forming Peptide GNNQQNY from the Yeast Prion Sup-35. Plos Comput. Biol.. 7:e1002051.
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2011. Mycoplasma gallisepticum produces a histone-like protein that recognizes base mismatches in DNA. Biochemistry. 50:8692–8702.
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2011. Non-monotonic dependence of water reorientation dynamics on surface hydrophilicity: competing effects of the hydration structure and hydrogen-bond strength. Phys. Chem. Chem. Phys.. 13:19911.
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2011. Optimizing the design of oligonucleotides for homology directed gene targeting. Plos One. 6:e14795.
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2011. Real Time Observation of Ultrafast Peptide Conformational Dynamics: Molecular Dynamics Simulation vs Infrared Experiment. J. Phys. Chem. B. 115:13084–13092.
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2011. Receptor Flexibility in Ligand Docking and Virtual Screening.. In-silico lead discovery.
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2011. Reorientation and Allied Dynamics in Water and Aqueous Solutions. Annu. Rev. Phys. Chem.. 62:395–416.
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2011. On the reorientation and hydrogen-bond dynamics of Alcohols. J. Phys. Chem. B. 115:12173–12178.
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2011. Role of packing, hydration and fluctuation on Thermostability. Thermostable Proteins Structural Stability and Design.
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2011. Simulation of the Oligomerization Pathway for Different Alloforms of the Amyloid Beta Protein Related to Alzheimer's Disease. Biophys. J.. 100:401.
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2011. Simulation of transient infrared spectra of a photoswitchable peptide. J. Chem. Phys.. 135
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2011. Water reorientation dynamics in the first hydration shells of F- and I-. Phys. Chem. Chem. Phys.. 13:19895.
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2011. X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel. Nature. 469:428–431.
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2010. Anharmonic torsional stiffness of DNA revealed under small external torques. Phys. Rev. Lett.. 105:018102.
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2010. An atomistic model for simulations of the general anesthetic isoflurane. J. Phys. Chem. B. 114:604–612.
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2010. A computational study of a recreated G protein-GEF reaction intermediate competent for nucleotide exchange: fate of the Mg ion. Plos One. 5:e9142.
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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.