目次

1. Computer-Aided Drug Design – An Overview Alan Talevi   2. Prediction of Human Drug Targets and their Interactions Using Machine Learning Methods: Current and Future Perspectives Abhigyan Nath, Priyanka Kumari, and Radha Chaube   3. Practices in Molecular Docking and Structure-based Virtual Screening Ricardo N. dos Santos, Leonardo G. Ferreira, and Adriano D. Andricopulo   4. Phylogenetic and Conservation Based Approaches to Predict Protein Functional Sites Heval Atas, Nurcan Tuncbag, and Tunca Doğan   5. De novo design of Ligands using Computational Methods Venkatesan Suryanarayanan, Umesh Panwar, Ishwar Chandra, and Sanjeev Kumar Singh   6. Molecular Dynamics Simulation and the Prediction of Druggable Binding Sites Tianhua Feng and Khaled Barakat   7. Virtual Ligand Screening using PL-PatchSurfer2, a Molecular Surface-based Protein-ligand Docking Method Woong-Hee Shin and Daisuke Kihara   8. Fragment Based Ligand Designing Shashank P. Katiyar, Vidhi Malik, Anjani Kumari, Kamya Singh,and Durai Sundar   9. Molecular Dynamics as a Tool for Virtual Ligand Screening Grégory Menchon, Laurent Maveyraud, and Georges Czaplicki   10. Building Molecular Interaction Networks from Microarray Data for Drug Target Screening Sze Chung Yuen, Hongmei Zhu, and Siu-wai Leung   11. Absolute Alchemical Free Energy Calculations for Ligand Binding Matteo Aldeghi, Joseph P. Bluck, and Philip C. Biggin   12. Evaluation of Protein-ligand Docking by Cyscore Yang Cao, Wentao Dai, and Zhichao Miao   13. 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 and Juan R. Perilla   14. Prediction and Optimization of Pharmacokinetic and Toxicity Properties of the Ligand Douglas E. V. Pires, Lisa M. Kaminskas, and David B. Ascher   15. Protein-protein Docking in Drug Design and Discovery Agnieszka A. Kaczor, Damian Bartuzi, Tomasz Maciej Stępniewski, and Dariusz Matosiuk, and Jana Selent 16. Automated Inference of Chemical Discriminants of Biological Activity Sebastian Raschka, Anne M. Scott, Mar Huertas, Weiming Li, and Leslie A. Kuhn   17. Computational Exploration of Conformational Transitions in Protein Drug Targets Benjamin P. Cossins and Alastair D. G. Lawson, Jiye Shi   18. Applications of the NRGsuite and the Molecular Docking Software FlexAID in Computational Drug Discovery and Design Louis-Philippe Morency, Francis Gaudreault, and Rafael Najmanovich   19. Calculation of Thermodynamic Properties of Bound Water Molecules Ying Yang, Amr Abdallah, and Markus A. Lill   20. Enhanced Molecular Dynamics Methods Applied to Drug Design Projects Sonia Ziada, Abdennour Braka, Julien Diharce, Samia Aci-Sèche, and Pascal Bonnet   21. AGGRESCAN3D: Towards the Prediction of the Aggregation Propensities of Protein Structures Jordi Pujols, Samuel Peña-Díaz, and Salvador Ventura   22. Computational Analysis of Solvent Inclusion in Docking Studies of Protein-glycosaminoglycan Systems Sergey A. Samsonov   23. Understanding G Protein-Coupled Receptor Allostery via Molecular Dynamics Simulations: Implications for Drug Discovery Shaherin Basith, Yoonji Lee, and Sun Choi   24. Identification of Potential Microrna Biomarkers by Meta-analysis Hongmei Zhu and Siu-wai Leung