Protein Structure Prediction

✍ Scribed by Daisuke Kihara

• Publisher: Springer US;Humana
• Year: 2020
• Tongue: English
• Leaves: 359
• Series: Methods in Molecular Biology 2165
• Edition: 4th ed.
• Category: Library

✦ Synopsis

This thorough new edition explores web servers and software for protein structure prediction and modeling that are freely available to the academic community. Taking into account the numerous advances in the computational protein structure prediction/modeling field, the book includes residue-contact prediction via deep learning, a wide variety of protein docking models, as well as cryo-electron microscopy (cryo-EM) techniques. Written by renowned experts in the field and for the highly successful Methods in Molecular Biology series, chapters include the kind of key detail and implementation advice necessary for researchers to achieve optimal results in their own work.
Authoritative and fully updated, Protein Structure Prediction, Fourth Edition is a practical and immediately useful guide for biology researchers working toward modeling protein structures.

✦ Table of Contents

Front Matter ....Pages i-xii
Structural Modeling and Ligand-Binding Prediction for Analysis of Structure-Unknown and Function-Unknown Proteins Using FORTE Alignment and PoSSuM Pocket Search (Yuko Tsuchiya, Kentaro Tomii)....Pages 1-11
The MULTICOM Protein Structure Prediction Server Empowered by Deep Learning and Contact Distance Prediction (Jie Hou, Tianqi Wu, Zhiye Guo, Farhan Quadir, Jianlin Cheng)....Pages 13-26
The Genome3D Consortium for Structural Annotations of Selected Model Organisms (Vaishali P. Waman, Tom L. Blundell, Daniel W. A. Buchan, Julian Gough, David Jones, Lawrence Kelley et al.)....Pages 27-67
Estimating the Quality of 3D Protein Models Using the ModFOLD7 Server (Ali H. A. Maghrabi, Liam J. McGuffin)....Pages 69-81
Prediction of Intrinsic Disorder with Quality Assessment Using QUARTER (Zhonghua Wu, Gang Hu, Christopher J. Oldfield, Lukasz Kurgan)....Pages 83-101
Modeling of Three-Dimensional RNA Structures Using SimRNA (Tomasz K. Wirecki, Chandran Nithin, Sunandan Mukherjee, Janusz M. Bujnicki, Michał J. Boniecki)....Pages 103-125
Modeling Protein Homo-Oligomer Structures with GalaxyHomomer Web Server (Minkyung Baek, Taeyong Park, Lim Heo, Chaok Seok)....Pages 127-137
Template-Based Modeling of Protein Complexes Using the PPI3D Web Server (Justas Dapkūnas, Česlovas Venclovas)....Pages 139-155
Protein–Protein and Protein–Peptide Docking with ClusPro Server (Andrey Alekseenko, Mikhail Ignatov, George Jones, Maria Sabitova, Dima Kozakov)....Pages 157-174
Modeling of Protein Complexes and Molecular Assemblies with pyDock (Mireia Rosell, Luis Angel Rodríguez-Lumbreras, Juan Fernández-Recio)....Pages 175-198
A Guide for Protein–Protein Docking Using SwarmDock (Iain H. Moal, Raphael A. G. Chaleil, Mieczyslaw Torchala, Paul A. Bates)....Pages 199-216
Modeling Protein–Protein or Protein–DNA/RNA Complexes Using the HDOCK Webserver (Yumeng Yan, Sheng-You Huang)....Pages 217-229
IDP-LZerD: Software for Modeling Disordered Protein Interactions (Charles Christoffer, Daisuke Kihara)....Pages 231-244
AnAnaS: Software for Analytical Analysis of Symmetries in Protein Structures (Guillaume Pagès, Sergei Grudinin)....Pages 245-257
MDockPeP: A Web Server for Blind Prediction of Protein–Peptide Complex Structures (Xianjin Xu, Xiaoqin Zou)....Pages 259-272
Protocols for All-Atom Reconstruction and High-Resolution Refinement of Protein–Peptide Complex Structures (Aleksandra E. Badaczewska-Dawid, Alisa Khramushin, Andrzej Kolinski, Ora Schueler-Furman, Sebastian Kmiecik)....Pages 273-287
Dockground Tool for Development and Benchmarking of Protein Docking Procedures (Petras J. Kundrotas, Ian Kotthoff, Sherman W. Choi, Matthew M. Copeland, Ilya A. Vakser)....Pages 289-300
Molecular Dynamics Flexible Fitting: All You Want to Know About Resolution Exchange (John W. Vant, Daipayan Sarkar, Chitrak Gupta, Mrinal S. Shekhar, Sumit Mittal, Abhishek Singharoy)....Pages 301-315
Protein Structure Modeling from Cryo-EM Map Using MAINMAST and MAINMAST-GUI Plugin (Genki Terashi, Yuhong Zha, Daisuke Kihara)....Pages 317-336
Protocols for Fast Simulations of Protein Structure Flexibility Using CABS-Flex and SURPASS (Aleksandra E. Badaczewska-Dawid, Andrzej Kolinski, Sebastian Kmiecik)....Pages 337-353
Back Matter ....Pages 355-358

✦ Subjects

Life Sciences; Protein Science; Bioinformatics; Chemistry/Food Science, general