Publications
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2020. Protein Interaction Energy Landscapes are Shaped by Functional and also Non-functional Partners.. J Mol Biol. 432(4):1183-1198.
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2007. Protein mechanics: a route from structure to function. Journal of Biosciences. 32:891–898.
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2013. Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information. Plos Comput. Biol.. 9:e1003369.
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2013. Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information. Plos Comput. Biol.. 9:e1003369.
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2018. Rayleigh-Plesset equation of the bubble stable cavitation in water: A nonequilibrium all-atom molecular dynamics simulation study. The Journal of Chemical Physics. 148:094505.
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2008. Recombination and Meiosis : Models, Means and Evolution Coll. Genome Dynamics \& Stability. Genome Dynamics \& Stability. 3:65–84.
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2010. A Rendering Method for Small Molecules up to Macromolecular Systems: HyperBalls Accelerated by Graphics Processors. JOBIM.
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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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2009. Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent.. J. Phys. Chem. B. 113:267–274.
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2009. Role of nucleic acid binding in Sir3p-dependent interactions with chromatin fibers.. Biochemistry. 48:276–288.
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2016. Salt-Excluding Artificial Water Channels Exhibiting Enhanced Dipolar Water and Proton Translocation. J. Am. Chem. Soc.. 138:5403–5409.
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2016. Salt-Excluding Artificial Water Channels Exhibiting Enhanced Dipolar Water and Proton Translocation. J. Am. Chem. Soc.. 138:5403–5409.
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2010. Sequence-dependent DNA flexibility mediates DNase I cleavage. J. Mol. Biol.. 395:123–133.
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2016. Sites of Anesthetic Inhibitory Action on a Cationic Ligand-Gated Ion Channel. Structure. 24a:595–605.
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2020. Scalable molecular dynamics on CPU and GPU architectures with NAMD. The Journal of Chemical Physics. 153
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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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2019. Slow extension of the invading DNA strand in a D-loop formed by RecA-mediated homologous recombination may enhance recognition of DNA homology. J Biol Chem. 294:8606-8616.
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2017. Small static electric field strength promotes aggregation-prone structures in amyloid-β(29-42).. J Chem Phys. 146(14):145101.
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2017. Smoothed biasing forces yield unbiased free energies with the extended-system Adaptive Biasing Force method. J. Phys. Chem. B. 121(15):3676–3685.
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2017. Smoothed biasing forces yield unbiased free energies with the extended-system Adaptive Biasing Force method. J. Phys. Chem. B. 121(15):3676–3685.
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1995. Solution structure of oligonucleotides covalently linked to a psoralen derivative.. Nucleic Acids Res.. 23:788–795.
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2004. Squash inhibitors: From structural motifs to macrocyclic knottins. Current Protein \& Peptide Science. 5:341–349.
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2018. A Streamlined, General Approach for Computing Ligand Binding Free Energies and Its Application to GPCR-Bound Cholesterol.. Journal of Chemical Theory and Computation. 14:6560–6573.