Publications
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2011. Dynamics of water in concentrated solutions of amphiphiles: Key roles of local structure and aggregation. J. Phys. Chem. B. 115:3254–3262.
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2011. Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the A beta(16-22) dimer and trimer. Phys. Chem. Chem. Phys.. 13:9778–9788.
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2011. Effects of G33A and G33I Mutations on the Structures of Monomer and Dimer of the Amyloid-beta Fragment 29-42 by Replica Exchange Molecular Dynamics Simulations. J. Phys. Chem. B. 115:1282–1288.
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2011. Electrostatically–driven fast association and perdeuteration allow transferred cross–relaxation detection for G protein–coupled receptor ligands with equilibrium dissociation constants in the high–to–low nanomolar range. J Biomolecular Nmr. 50:191–5.
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2011. Enzyme Closure and Nucleotide Binding Structurally Lock Guanylate Kinase. Biophys. J.. 101:1440–1449.
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2011. Exploring the energy landscape of small peptides and proteins by molecular dynamics simulations.
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2011. From toxins targeting ligand gated ion channels to therapeutic molecules. Toxins (basel). 3:260–293.
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2011. Frontier residues lining globin internal cavities present specific mechanical properties. J. Am. Chem. Soc.. 133:8753–8761.
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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.