Publications
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2015. Content and task based navigation for structural biology in 3D environments. Virtual and Augmented Reality for Molecular Science (VARMS@IEEEVR), 2015 IEEE 1st International Workshop on. :31–36.
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2015. Docking Peptides on Proteins: How to Open a Lock, in the Dark, with a Flexible Key. Structure. 23:1373–1374.
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2015. Epock: rapid analysis of protein pocket dynamics. Bioinformatics. 31:1478–1480.
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2015. The elastic free energy of a tandem modular protein under force.. Biochem. Biophys. Res. Comm.. :1–5.
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2015. Fold and flexibility: what can proteins' mechanical properties tell us about their folding nucleus? J. R. Soc. Interface. 12
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2015. Folding Atomistic Proteins in Explicit Solvent Using Simulated Tempering. J. Phys. Chem. B. 119:6941–6951.
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2015. How osmolytes influence hydrophobic polymer conformations: A unified view from experiment and theory.. Proc. Natl. Acad. Sci. Usa. 112:9270–5.
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2015. Inhibition of protein aggregation and amyloid formation by small molecules. Curr. Opin. Struct. Biol.. 30:50–56.
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2015. Integrating multi-scale data on homologous recombination into a new recognition mechanism based on simulations of the RecA-ssDNA/dsDNA structure. Nucleic Acids Res.. 43:10251–63.
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2015. An integrative approach to the study of filamentous oligomeric assemblies, with application to RecA. Plos One. in press:e0116414.
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2015. Investigating the Structural Variability and Binding Modes of the Glioma Targeting NFL-TBS.40-63 Peptide on Tubulin. Biochemistry. 54:3660–3669.
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2015. Allosteric and hyperekplexic mutant phenotypes investigated on an α1 glycine receptor transmembrane structure. Proc. Natl. Acad. Sci. U.s.a.. 112:2865–2870.
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2015. The mechanochemistry of copper reports on the directionality of unfolding in model cupredoxin proteins.. Nature Comm.. 6:7894.
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2015. Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory.. J. Membr. Biol.. 248
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2015. Molecular structure of the NQTrp inhibitor with the Alzheimer A beta 1-28 monomer. Eur. J. Med. Chem.. 91:43–50.
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2015. Nothing to sneeze at: a dynamic and integrative computational model of an influenza A virion. Structure. 23:584–597.
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2015. Predicting and exploring complex nucleic acids architectures through a coarse-grained model. J. Biomol. Struct. Dyn.. 33 Suppl 1:30–31.
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2015. Picosecond dissociation of amyloid fibrils with infrared laser: A nonequilibrium simulation study. J. Chem. Phys.. 143:155101.
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2015. Picosecond melting of peptide nanotubes using an infrared laser: a nonequilibrium simulation study. Phys. Chem. Chem. Phys.. 17:27275–27280.
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2015. The poor homology stringency in the heteroduplex allows strand exchange to incorporate desirable mismatches without sacrificing recognition in vivo. Nucleic Acids Res.. 43:6473–85.
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2015. Predicting and exploring complex nucleic acids architectures through a coarse-grained model. Journal of Biomolecular Structure & Dynamics. 33:30–31.
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2015. Protein Simulations in Fluids: Coupling the OPEP Coarse-Grained Force Field with Hydrodynamics. J. Chem. Theory Comput.. 11:1843–1853.
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2015. Recovering protein thermal stability using all-atom Hamiltonian replica-exchange simulations in explicit solvent. J. Chem. Theo. Comput.. 11:5573–5577.
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2015. Replica-exchange molecular dynamics simulation for understanding the initial process of amyloid peptide aggregation. Mol. Simul.. 41:1041–1044.
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2015. Role of Internal Water on Protein Thermal Stability: The Case of Homologous G Domains.. J. Phys. Chem. B. 119:8939–49.