Computational Peptidology, Softcover reprint of the original 1st ed. 2015 Methods in Molecular Biology Series, Vol. 1268

In this volume expert researchers detail in silico methods widely used to study peptides. These include methods and techniques covering the database, molecular docking, dynamics simulation, data mining, de novo design and structure modeling of peptides and protein fragments. Chapters focus on integration and application of technologies to analyze, model, identify, predict, and design a wide variety of bioactive peptides, peptide analogues and peptide drugs, as well as peptide-based biomaterials. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls.

Authoritative and practical, Computational Peptidology seeks to aid scientists in the further study into this newly rising subfield.

1. De Novo Peptide Structure Prediction: An Overview

Pierre Thévenet, Julien Rey, Gautier Moroy, and Pierre Tuffery

2. Molecular Modeling of Peptides

Krzysztof Kuczera

3. Improved Methods for Classification, Prediction, and Design of Antimicrobial Peptides

Guangshun Wang

4. Building MHC Class II Epitope Predictor Using Machine Learning Approaches

Loan Ping Eng, Tin Wee Tan, And Joo Chuan Tong

5. Brownian Dynamics Simulation Of Peptides with The University of Houston Brownian Dynamics (UHBD) Program

Tongye Shen and Chung F. Wong

6. Computational Prediction of Short Linear Motifs from Protein Sequences

Richard J. Edwards And Nicolas Palopoli

7. Peptide Toxicity Prediction

Sudheer Gupta, Pallavi Kappor, Kumardeep Chaudhary, Ankur Gautam, Rahul Kumar, Gajendra P.S. Raghava

8. Synthetica Structural Routes For The Rational Conversion of Peptides Into Small Molecules

Pasqualina Liana Scognamiglio, Giancarlo Morelli, and Daniela Marasco

9. In Silico Design Of Antimicrobial Peptides

Giuseppe Maccari, Mariagrazia Di Luca, and Riccardo Nifosì

10. Information-Driven Modelling Of Protein-Peptide Complexes

“Information-Driven Peptide Docking”

Mikael Trellet, Adrien S.J. Melquiond, and Alexandre M.J.J. Bonvin

Fergal J. Duffy, Marc Devocelle, and Denis C. Shields

12. A Use of Homology Modeling And Molecular Docking Methods: To Explore Binding Mechanisms of Nonylphenol And Bisphenol a with Antioxidant Enzymes

Mannu Jayakanthan, Rajamanickam Jubendradass, Shereen Cynthia D’Cruz, and Premendu P. Mathur

Johannes Söllner

14. Computational Modeling Of Peptide-Aptamer Binding

Kristen L. Rhinehardt, Ram V. Mohan, and Goundla Srinivas

Includes cutting-edge methods and protocols

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts