(PDF) In Silico Drug Discovery and Design by Claudio N. Cavasotto

This is the PDF eBook version for In Silico Drug Discovery and Design – Theory, Methods, Challenges, and Applications by Claudio N. Cavasotto

Table of Contents

The Physical Basis of Ligand Binding
Thomas Simonson
Force-Field Representation of Biomolecular Systems
Meagan C. Small and Alexander D. MacKerell, Jr.
Library Design, Chemical Space, and Drug Likeness
Hugo O. Villar
Ligand-Based Drug Discovery and Design
Álvaro Cortés-Cabrera, Pedro A. Sánchez Murcia, Antonio Morreale, and Federico Gago
Pharmacophore Modeling and Pharmacophore-Based Virtual Screening
Muhammad Akram, Teresa Kaserer, and Daniela Schuster
Protein-Ligand Docking: From Basic Principles to Advanced Applications
Christoph A. Sotriffer
Protein-Ligand Docking: Virtual Screening and Applications to Drug Discovery
Antonella Ciancetta and Stefano Moro
Protein Structure Modeling in Drug Design
Damián Palomba and Claudio N. Cavasotto
Implicit Solvation Methods in the Study of Ligand-Protein Interactions
William Zamora, Josep M. Campanera, and F. Javier Luque
Toward Complete Cellular Pocketomes and Predictive Polypharmacology
Ruben A. Abagyan and Bryn Taylor
MM-GB/SA Rescoring of Docking Poses: Tricks of the Trade
Cristiano R. W. Guimarães
Free Energy Calculations of Ligand-Protein Binding
Rainer Bomblies, Manuel Luitz, and Martin Zacharias
Molecular Mechanics/Coarse-Grained Simulations as a Structural Prediction Tool for GPCRs/Ligand Complexes
Francesco Musiani, Alejandro Giorgetti, and Paolo Carloni
Fragment-Based Methods in Drug Design
Márton Vass, Gergely Makara, and György Miklós Keseru
Role of Water Molecules and Hydration Properties in Modeling Ligand-Protein Interaction and Drug Design
Alfonso T. García-Sosa
How Protein Flexibility Can Influence Docking/Scoring Simulations
Pietro Cozzini, Luca Dellafiora, Tiziana Ginex, and Francesca Spyrakis
In Silico Approaches Assisting the Rational Design of Low Molecular Weight Protein-Protein Interaction Modulators
Bruno O. Villoutreix, Melaine A. Kuenemann, David Lagorce, Olivier Sperandio, and Maria A. Miteva
Incorporating Binding Kinetics in Drug Design
Chung F. Wong