Computational Drug Discovery and Design

A Molecular Dynamics Ensemble-Based Approach for the Mapping of Druggable Binding Sites.-Analysis of Protein Binding Sites by Computational Solvent Mapping.-Evolutionary Trace for Prediction and Redesign of Protein Functional Sites.- Information Entropic Functions for Molecular Descriptor Profiling.-Expanding the Conformational Selection Paradigm in Protein-Ligand Docking.-Flexibility Analysis of Biomacromolecules with Application to Computer-aided Drug Design.-On the Use of Molecular Dynamics Receptor Conformations for Virtual Screening.-Virtual Ligand Screening Against Comparative Protein Structure Models.-AMMOS Software: Method and Application.-Rosetta Ligand Docking with Flexible XML Protocols.-Normal Mode-Based Approaches in Receptor Ensemble Docking.-Application of Conformational Clustering in Protein-Ligand Docking.-How to Benchmark Methods for Structure-based Virtual Screening of Large Compound Libraries.-AGGRESCAN: Method, Application, and Perspectives for Drug Design.-ATTRACT and PTOOLS: Open Source Programs for Protein-protein Docking.-Prediction of Interacting Protein Residues using Sequence and Structure Data.-MM-GB/SA Rescoring of Docking Poses.-A Case Study of Scoring and Rescoring in Peptide Docking.-The Solvated Interaction Energy (SIE) Method for Scoring Binding Affinities.-Linear Interaction Energy (LIE): Method and Applications in Drug Design.-Estimation of Conformational Entropy in Protein-Ligand Interactions: a Computational Perspective.-Explicit Treatment of Water Molecules in Data-driven Protein-protein Docking: The Solvated HADDOCKing Approach.Protein–water Interactions in MD Simulations: POPS/POPSCOMP Solvent Accessibility Analysis, Solvation Forces and Hydration Sites.-Computing the Thermodynamic Contributions of Interfacial Water.-Assignment of Protonation States in Proteins and Ligands: Combining pKa Prediction with Hydrogen Bonding Network Optimization.-Best Practices in Free Energy Calculations for DrugDesign.-Independent-Trajectory Thermodynamic Integration:A Practical Guide to Protein-Drug Binding Free Energy Calculations Using Distributed Computing.- Free Energy Calculations from One-step Perturbations.-Using Metadynamics and Path Collective Variables to Study Ligand Binding and Induced Conformational Transitions.-Accelerated Molecular Dynamics In Computational Drug Design.-Molecular Dynamics Applied in Drug Discovery: the Case of HIV-1 Protease.-Decomposing the Energetic Impact of Drug-Resistant Mutations: The Example of HIV-1 Protease-DRV Binding.-Virtual Screening Helps Experiment Design: Application to the Akt Phosphatase PHLPP.- Molecular-Level Simulation of Pandemic Influenza Glycoproteins.-Homology Modeling of Cannabinoid Receptor: Discovery of Cannabinoid Analogues for Therapeutic Use.-High-throughput Virtual Screening Lead to Discovery of Non-peptidic Inhibitors of West Nile Virus NS3 Protease.