Publications
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2016. Non-equivalent binding sites for Abeta1-40 on PrP determine the oligomerisation pathway. Prion. 10:S40.
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2016. PEP-FOLD3: faster denovo structure prediction for linear peptides in solution and in complex. Nucleic Acids Res.. 44:W449-W454.
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2016. Picosecond infrared laser-induced all-atom nonequilibrium molecular dynamics simulation of dissociation of viruses. Phys. Chem. Chem. Phys.. 18:11951–11958.
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2016. Toward Microscopic Simulations of Proteins in Cell-Like Environments. Biophys. J.. 110:386A.
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2015. Ab initio RNA folding. Journal of Physics-condensed Matter. 27:233102.
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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. 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.. The Journal of Chemical Physics. 143:021101–021101.
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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. Epock: rapid analysis of protein pocket dynamics. Bioinformatics. 31:1478–1480.
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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. Inhibition of protein aggregation and amyloid formation by small molecules. Curr. Opin. Struct. Biol.. 30:50–56.
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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. 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. 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. Replica-exchange molecular dynamics simulation for understanding the initial process of amyloid peptide aggregation. Mol. Simul.. 41:1041–1044.
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2015. Structures of the Alzheimer’s Wild-Type A beta 1-40 Dimer from Atomistic Simulations. J. Phys. Chem. B. 119:10478–10487.
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2015. UnityMol: interactive and ludic visual manipulation of coarse-grained RNA and other biomolecules. Virtual and Augmented Reality for Molecular Science (VARMS@IEEEVR), 2015 IEEE 1st International Workshop on. :1–6.
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2015. What Computational Methods can Teach us about the Alzheimer-Protective Nature of A2V-and A2T-Mutant Amyloid-Beta Oligomers. Biophys. J.. 108:204A-204A.
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2014. Amyloid oligomer structure characterization from simulations: A general method. J. Chem. Phys.. 140:094105.