Computational Drug Discovery and Design

Front Matter

Computer-Aided Drug Design: An Overview

• Alan Talevi

Prediction of Human Drug Targets and Their Interactions Using Machine Learning Methods: Current and Future Perspectives

• Abhigyan Nath, Priyanka Kumari, Radha Chaube

Practices in Molecular Docking and Structure-Based Virtual Screening

• Ricardo N. dos Santos, Leonardo G. Ferreira, Adriano D. Andricopulo

Phylogenetic and Other Conservation-Based Approaches to Predict Protein Functional Sites

• Heval Atas, Nurcan Tuncbag, Tunca Doğan

De Novo Design of Ligands Using Computational Methods

• Venkatesan Suryanarayanan, Umesh Panwar, Ishwar Chandra, Sanjeev Kumar Singh

Molecular Dynamics Simulation and Prediction of Druggable Binding Sites

• Tianhua Feng, Khaled Barakat

Virtual Ligand Screening Using PL-PatchSurfer2, a Molecular Surface-Based Protein–Ligand Docking Method

• Woong-Hee Shin, Daisuke Kihara

Fragment-Based Ligand Designing

• Shashank P. Katiyar, Vidhi Malik, Anjani Kumari, Kamya Singh, Durai Sundar

Molecular Dynamics as a Tool for Virtual Ligand Screening

• Grégory Menchon, Laurent Maveyraud, Georges Czaplicki

Building Molecular Interaction Networks from Microarray Data for Drug Target Screening

• Sze Chung Yuen, Hongmei Zhu, Siu-wai Leung

Absolute Alchemical Free Energy Calculations for Ligand Binding: A Beginner’s Guide

• Matteo Aldeghi, Joseph P. Bluck, Philip C. Biggin

Evaluation of Protein–Ligand Docking by Cyscore

• Yang Cao, Wentao Dai, Zhichao Miao

Molecular Dynamics Simulations of Protein–Drug Complexes: A Computational Protocol for Investigating the Interactions of Small-Molecule Therapeutics with Biological Targets and Biosensors

• Jodi A. Hadden, Juan R. Perilla

Prediction and Optimization of Pharmacokinetic and Toxicity Properties of the Ligand

• Douglas E. V. Pires, Lisa M. Kaminskas, David B. Ascher

Protein–Protein Docking in Drug Design and Discovery

• Agnieszka A. Kaczor, Damian Bartuzi, Tomasz Maciej Stępniewski, Dariusz Matosiuk, Jana Selent

Automated Inference of Chemical Discriminants of Biological Activity

• Sebastian Raschka, Anne M. Scott, Mar Huertas, Weiming Li, Leslie A. Kuhn

Computational Exploration of Conformational Transitions in Protein Drug Targets

• Benjamin P. Cossins, Alastair D. G. Lawson, Jiye Shi

Applications of the NRGsuite and the Molecular Docking Software FlexAID in Computational Drug Discovery and Design

• Louis-Philippe Morency, Francis Gaudreault, Rafael Najmanovich

Calculation of Thermodynamic Properties of Bound Water Molecules

• Ying Yang, Amr H. A. Abdallah, Markus A. Lill