In Silico Models for Drug Discovery, 2013
Methods in Molecular Biology Series, Vol. 993

Infectious diseases caused by viruses, parasites, bacteria, and fungi are the number one cause of death worldwide. Although new technologies have improved diagnosis of infectious diseases, the efficacy of all known current anti-infective agents is threatened by the spread of drug-resistant forms of the pathogens. Hence, there remains an urgent need to develop anti-infective agents that target drug-resistant pathogens. In Silico Models for Drug Discovery presents a comprehensive look at the role in silico models play in understanding infectious diseases and in developing novel therapeutics to treat them. Written by leading experts in the field, chapters cover topics such as techniques to derive novel antimicrobial targets, methods of interpreting polypharmacology-based drug target networks, and molecular dynamics techniques used to compute binding energies of drugs to their target proteins, to name a few. Written in the successful Methods in Molecular Biology? series or in review article format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls.

Authoritative and easily accessible, In Silico Models for Drug Discovery seeks to serve both professionals and novices involved in the study and treatment of infectious diseases.

1. Virtual Screening in Drug Design

Markus Lill

2. In Silico Systems Biology Approaches for the Identification of Antimicrobial Targets

Malabika Sarker, Carolyn Talcott, and Amit K. Galande

3. Genome Comparisons as a Tool for Antimicrobial Target Discovery

Hong Sun, Hai-Feng Chen, and Runsheng Chen

4. In Silico Models for Drug Resistance

Segun Fatumo, Marion Adebiyi, and Ezekiel Adebiyi

5. An In Silico Model for Interpreting Polypharmacological Relationships in Drug-Target Networks

Ichigaku Takigawa, Koji Tsuda, and Hiroshi Mamitsuka

6. On Exploring Structure–Activity Relationships

Rajarshi Guha

7. Molecular Dynamics Simulations in Drug Design

John E. Kerrigan

8. Databases and In Silico Tools for Vaccine Design

Yongqun He and Zuoshuang Xiang

9. In Silico Models for B-Cell Epitope Recognition and Signaling

Hifzur Rahman Ansari and Gajendra P.S. Raghava

10. The Collaborative Drug Discovery (CDD) Database

Sean Ekins and Barry A. Bunin

11. Recognition of Nontrivial Remote Homology Relationships Involving Proteins of Helicobacter pylori: Implications for Function Recognition

Nidhi Tyagi and Narayanaswamy Srinivasan

12. Identification of Novel Anthrax Toxin Countermeasures Using In Silico Methods

Ting-Lan Chiu, Kimberly M. Maize, and Elizabeth A. Amin

13. Rational Design of HIV-1 Entry Inhibitors

Asim K. Debnath

14. Malarial Kinases: Novel Targets for In Silico Approaches to Drug Discovery

Kristen M. Bullard, Robert Kirk DeLisle, and Susan M. Keenan

15. Designing Novel Inhibitors of Trypanosoma brucei

Özlem Demir and Rommie E. Amaro

16. Computational Models for Tuberculosis Drug Discovery

Sean Ekins and Joel S. Freundlich

Rajarshi Guha

7. Molecular Dynamics Simulations in Drug Design

John E. Kerrigan

8. Databases and In Silico Tools for Vaccine Design

Yongqun He and Zuoshuang Xiang

9. In Silico Models for B-Cell Epitope Recognition and Signaling

Hifzur Rahman Ansari and Gajendra P.S. Raghava

10. The Collaborative Drug Discovery (CDD) Database

Sean Ekins and Barry A. Bunin

11. Recognition of Nontrivial Remote Homology Relationships Involving Proteins of Helicobacter pylori: Implications for Function Recognition

Nidhi Tyagi and Narayanaswamy Srinivasan

12. Identification of Novel Anthrax Toxin Countermeasures Using In Silico Methods

Ting-Lan Chiu, Kimberly M. Maize, and Elizabeth A. Amin

13. Rational Design of HIV-1 Entry Inhibitors

Asim K. Debnath

14. Malarial Kinases: Novel Targets for In Silico Approaches to Drug Discovery

Kristen M. Bullard, Robert Kirk DeLisle, and Susan M. Keenan

15. Designing Novel Inhibitors of Trypanosoma brucei

Özlem Demir and Rommie E. Amaro

16. Computational Models for Tuberculosis Drug Discovery

Sean Ekins and Joel S. Freundlich

Includes cutting-edge methods and protocols

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts

Includes supplementary material: sn.pub/extras