Structural Bioinformatics: Methods and Protocols

ISBN-13: 9781071602690 / Angielski / Twarda / 2020 / 256 str.

Zoltan Gaspari

Spis treści

Preface…

Table of Contents…

Contributing Authors…

1. Visualization and Analysis of Protein Structures with LiteMol Suite

David Sehnal, Radka Svobodová, Karel Berka, Lukáš Pravda, Adam Midlik, and Jaroslav Koča

2 Comparative Protein Structure Analysis with Bio3D-Web

Barry J. Grant, Lars Skjærven, and Xin-Qiu Yao

3 Using DALI for Protein Structure Comparison

Liisa Holm

4. Assessing Protein Function through Structural Similarities with CATH

Natalie L. Dawson, Christine Orengo, and Zoltán Gáspári

5 Protein Thermal Stability Engineering using HoTMuSiC

Fabrizio Pucci, Jean Marc Kwasigroch, and Marianne Rooman

6 Contact Area-Based Structural Analysis of Proteins and their Complexes using CAD-Score

Kliment Olechnovič, and Česlovas Venclovas

7 A Comprehensive Computational Platform to Guide Drug Development using Graph-Based Signature Methods

Douglas E. V. Pires, Stephanie Portelli, Pâmela M. Rezende, Wandré N. P. Veloso, Joicymara S. Xavier, Malancha Karmakar, Yoochan Myung, João P. V. Linhares, Carlos H. M. Rodrigues, Michael Silk, and David B. Ascher

8 Systematic Exploration of Binding Modes of Ligands on Drug Targets

Csaba Hetényi and Mónika Bálint

9. Using MemBlob to Analyze Transmembrane Regions Based on Cryo-EM Maps

Georgina Csizmadia, Bianka Farkas, Eszter Katona, Gábor E. Tusnády, and Tamás Hegedűs

10 Structural Characterization of Protein-Protein Interactions with pyDockSAXS

Brian Jiménez-García, Pau Bernadó, and Juan Fernández-Recio

11 Protein-Protein Modeling using Cryo-EM Restraints

Mikael Trellet, Gydo van Zundert, and Alexandre M.J.J. Bonvin

12 Modeling of Multimolecular Complexes

Dina Schneidman-Duhovny and Haim J. Wolfson

13 Biological Assembly Comparison with VAST+

Thomas Madej, Aron Marchler-Bauer, Christopher Lanczycki, Dachuan Zhang, and Stephen H. Bryant

14 BioMagResBank (BMRB) as a Resource for Structural Biology

Pedro R. Romero, Naohiro Kobayashi, Jonathan Wedell, Kumaran Baskaran, Takeshi Iwata, Masashi Yokochi, Dimitri Maziuk, Hongyang Yao, Toshimichi Fujiwara, Genji Kurisu, Eldon L. Ulrich, Jeffrey C. Hoch, and John L. Markley

15 Integrating Molecular Simulation and Experimental Data: A Bayesian/Maximum Entropy Reweighting Approach

Sandro Bottaro, Tone Bengtsen, and Kresten Lindorff-Larsen

16 Evaluation and Selection of Dynamic Protein Structural Ensembles with CoNSEnsX+

Dániel Dudola, Bertalan Kovács, and Zoltán Gáspári

Blurb

This volume looks at the latest techniques used to perform comparative structure analyses, and predict and evaluate protein-ligand interactions. The chapters in this book cover tools and servers such as LiteMol; Bio3D-Web; DALI; CATH; HoTMuSiC, a contact-base protein structure analysis tool known as CAD-Score; PyDockSaxs and HADDOCK; CombDock and DockStar; the BioMagResBank database; as well as BME and CoNSEnsX+. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible computational protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and comprehensive, Structural Bioinformatics: Methods and Protocols is a practical guide for researchers to learn more about the aforementioned tools to further enhance their studies in the growing field of structural bioinformatics.

Chapter 13 is open access under a CC-BY 4.0 license via link.springer.com.