Publications
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2016. Toward Microscopic Simulations of Proteins in Cell-Like Environments. Biophys. J.. 110:386A.
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2016. Visual Analysis of Biomolecular Cavities: State of the Art. Comput. Graphics Forum. 35:527–551.
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2016. Visualization of Biomolecular Structures: State of the Art Revisited. Comput. Graphics Forum.
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2016. Water Determines the Structure and Dynamics of Proteins. Chem. Rev.. 116:7673–7697.
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2015. Ab initio RNA folding. Journal of Physics-condensed Matter. 27:233102.
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2015. The adaptive biasing force method: everything you always wanted to know but were afraid to ask.. J. Phys. Chem. B. 119:1129–51.
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2015. Algebraic Statistics of Poincaré Recurrences in a DNA Molecule.. Phys. Rev. Lett.. 115:188104.
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2015. Amyloid beta Protein and Alzheimer’s Disease: When Computer Simulations Complement Experimental Studies. Chem. Rev.. 115:3518–3563.
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2015. Are coarse-grained models apt to detect protein thermal stability? The case of \OPEP\ force field J. Non-cryst. Solids. 407:494–501.
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2015. Changes in protein structure at the interface accompanying complex formation.. Iucrj. 2:643–652.
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2015. Coarse-Grained HiRE-RNA Model for ab Initio RNA Folding beyond Simple Molecules, Including Noncanonical and Multiple Base Pairings. J. Chem. Theory Comput.. 11:3510–3522.
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2015. Combined Experimental and Simulation Studies Suggest a Revised Mode of Action of the Anti-Alzheimer Disease Drug NQ-Trp. Chemistry-a European Journal. 21:12657–12666.
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2015. Communication: Multiple atomistic force fields in a single enhanced sampling simulation. J. Chem. Phys.. 143:021101.
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2015. Communication: Multiple atomistic force fields in a single enhanced sampling simulation.. The Journal of Chemical Physics. 143:021101–021101.
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2015. Conformational ensembles and sampled landscapes: analysis and comparison. J. Comp. Chem.. 36:1213–31.
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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.