Protein-Ligand Interactions and Drug Design

Investigation of the Click-Chemical Space for Drug Design Using ZINClick.- Molecular Scaffold Hopping via Holistic Molecular Representation.- Biased Docking for Protein-Ligand Pose Prediction.- Binding Mode Prediction and Virtual Screening Applications by Covalent Docking.- Ligand-Receptor, Ligand-DNA Interactions and Drug Design.- Simulation of Ligand Transport in Receptors Using CaverDock.- Negative Image-Based Screening: Rigid Docking Using Cavity Information.- Negative Image-Based Rescoring: Using Cavity Information to Improve Docking Screening.- Fragment-Based Drug Design of Selective HDAC6 Inhibitors.- A Protocol to Use Comparative Binding Energy Analysis to Estimate Drug-Target Residence Time.- Dynamic Docking Using Multicanonical Molecular Dynamics: Simulating Complex Formation at the Atomistic Level.- Free Energy Calculations for Protein-Ligand Binding Prediction.- Exploiting Water Dynamics for Pharmacophore Screening.- Markov State Models to Elucidate Ligand Binding Mechanism.- From Homology Modeling to the Hit Identification and Drug Repurposing: A Structure-Based Approach in the Discovery of Novel Potential Anti-Obesity Compounds.- Multiple Target Drug Design Using LigBuilder 3.- Bionoi: A Voronoi Diagram-Based Representation of Ligand-Binding Sites in Proteins for Machine Learning Applications.- MDock: A Suite for Molecular Inverse Docking and Target Prediction.