Computational Drug Discovery and Design
(Book #1762 in the Methods in Molecular Biology Series)
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Book Overview
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
Gr?gory 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 CyscoreYang 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-S?che, and Pascal Bonnet
21. AGGRESCAN3D: Towards the Prediction of the Aggregation Propensities of Protein Structures
Jordi Pujols, Samuel Pe?a-D?az, 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
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