Description
Book SynopsisThis 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 isavailable open access under a CC-BY 4.0 license via link.springer.
Table of ContentsPreface…Table of Contents…Contributing Authors…
1. Visualization and Analysis of Protein Structures with LiteMol SuiteDavid Sehnal, Radka Svobodová, Karel Berka, Lukáš Pravda, Adam Midlik, and Jaroslav Koča
2 Comparative Protein Structure Analysis with Bio3D-WebBarry J. Grant, Lars Skjærven, and Xin-Qiu Yao
3 Using DALI for Protein Structure ComparisonLiisa Holm
4. Assessing Protein Function through Structural Similarities with CATHNatalie L. Dawson, Christine Orengo, and Zoltán Gáspári
5 Protein Thermal Stability Engineering using HoTMuSiCFabrizio Pucci, Jean Marc Kwasigroch, and Marianne Rooman
6 Contact Area-Based Structural Analysis of Proteins and their Complexes using CAD-ScoreKliment Olechnovič, and Česlovas Venclovas
7 A Comprehensive Computational Platform to Guide Drug Development using Graph-Based Signature MethodsDouglas 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 TargetsCsaba Hetényi and Mónika Bálint
9. Using MemBlob to Analyze Transmembrane Regions Based on Cryo-EM MapsGeorgina Csizmadia, Bianka Farkas, Eszter Katona, Gábor E. Tusnády, and Tamás Hegedűs
10 Structural Characterization of Protein-Protein Interactions with pyDockSAXSBrian Jiménez-García, Pau Bernadó, and Juan Fernández-Recio
11 Protein-Protein Modeling using Cryo-EM RestraintsMikael Trellet, Gydo van Zundert, and Alexandre M.J.J. Bonvin
12 Modeling of Multimolecular ComplexesDina 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 BiologyPedro 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 ApproachSandro 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
