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E-raamat: In Silico Models for Drug Discovery

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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.



Preface v
Acknowledgments vii
Contributors xi
1 Virtual Screening in Drug Design
1(12)
Markus Lill
2 In Silico Systems Biology Approaches for the Identification of Antimicrobial Targets
13(18)
Malabika Sarker
Carolyn Talcott
Amit K. Galande
3 Genome Comparisons as a Tool for Antimicrobial Target Discovery
31(8)
Hong Sun
Hai-Feng Chen
Runsheng Chen
4 In Silico Models for Drug Resistance
39(28)
Segun Fatumo
Marion Adebiyi
Ezekiel Adebiyi
5 An In Silico Model for Interpreting Polypharmacology in Drug-Target Networks
67(14)
Ichigaku Takigawa
Koji Tsuda
Hiroshi Mamitsuka
6 On Exploring Structure-Activity Relationships
81(14)
Rajarshi Guha
7 Molecular Dynamics Simulations in Drug Design
95(20)
John E. Kerrigan
8 Databases and In Silico Tools for Vaccine Design
115(14)
Yongqun He
Zuoshuang Xiang
9 In Silico Models for B-Cell Epitope Recognition and Signaling
129(10)
Hifzur Rahman Ansari
Gajendra P.S. Raghava
10 The Collaborative Drug Discovery (CDD) Database
139(16)
Sean Ekins
Barry A. Bunin
11 Recognition of Nontrivial Remote Homology Relationships Involving Proteins of Helicobacter pylori: Implications for Function Recognition
155(22)
Nidhi Tyagi
Narayanaswamy Srinivasan
12 Identification of Novel Anthrax Toxin Countermeasures Using In Silico Methods
177(8)
Ting-Lan Chiu
Kimberly M. Maize
Elizabeth A. Amin
13 Rational Design of HIV-1 Entry Inhibitors
185(20)
Asim K. Debnath
14 Malarial Kinases: Novel Targets for In Silico Approaches to Drug Discovery
205(26)
Kristen M. Bullard
Robert Kirk DeLisle
Susan M. Keenan
15 Designing Novel Inhibitors of Trypanosoma brucei
231(14)
Ozlem Demir
Rommie E. Amaro
16 Computational Models for Tuberculosis Drug Discovery
245(18)
Sean Ekins
Joel S. Freundlich
Index 263