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We study protein folding, amyloid aggregation, ligand docking, and complex networks.

Molecular Dynamics Simulations of Bromodomains Reveal Binding-Site Flexibility and Multiple Binding Modes of the Natural Ligand Acetyl-Lysine Experimental and Computational Study of BODIPY Dye-Labeled Cavitand Dynamics Equilibrium Sampling Approach to the Interpretation of Electron Density Maps. Mechanism and Kinetics of Acetyl-Lysine Binding to Bromodomains A scalable algorithm to order and annotate continuous observations reveals the metastable states visited by dynamical systems Kinetic response of a photoperturbed allosteric protein. Does bromodomain flexibility influence histone recognition? New Insights into the Folding of a β-Sheet Miniprotein in a Reduced Space of Collective Hydrogen Bond Variables: Application to a Hydrodynamic Analysis of the Folding Flow. Macrodomain-containing proteins are new mono-ADP-ribosylhydrolases. Carnosine Inhibits Aβ(42) Aggregation by Perturbing the H-Bond Network in and around the Central Hydrophobic Cluster. Methylations of Tryptophan Modified Naphtoquinone Affect Its Inhibitory Potential Towards Aβ Aggregation. Optimization of Inhibitors of the Tyrosine Kinase EphB4. 2. Cellular Potency Improvement and Binding Mode Validation by X-ray Crystallography. Distribution of Reciprocal of Interatomic Distances: A Fast Structural Metric Discovery of a novel chemotype of tyrosine kinase inhibitors by fragment-based docking and molecular dynamics Peptide binding to the PDZ3 domain by conformational selection. Discovery of Tyrosine Kinase Inhibitors by Docking into an Inactive Kinase Conformation Generated by Molecular Dynamics. Free Energy Guided Sampling How Does Darunavir Prevent HIV-1 Protease Dimerization? Mechanisms and kinetics of amyloid aggregation investigated by a phenomenological coarse-grained model Ultrametricity in Protein Folding Dynamics