Protein Structure Prediction

ISBN-13: 9781071607107 / Angielski / Miękka / 2021 / 358 str.

Daisuke Kihara

Spis treści

1. Structural Modeling and Ligand Binding Prediction for Analysis of Structure-Unknown and Function-Unknown Proteins Using FORTE Alignment and PoSSuM Pocket Search

            Yuko Tsuchiya and Kentaro Tomii

 

2. The MULTICOM Protein Structure Prediction Server Empowered by Deep Learning and Contact Distance Prediction

            Jie Hou, Tianqi Wu, Zhiye Guo, Farhan Quadir, and Jianlin Cheng

 

3. ­The Genome3D Consortium for Structural Annotations of Selected Model Organisms

            Vaishali P. Waman, Tom L. Blundell, Daniel Buchan, Julian Gough, David Jones, Lawrence Kelley, Alexey Murzin, Arun Prasad Pandurangan, Ian Sillitoe, Michael Sternberg, Pedro Torres, and Christine Orengo

 

4. Estimating the Quality of 3D Protein Models Using the ModFOLD7 Server

            Ali H.A. Maghrabi and Liam J. McGuffin

 

5. Prediction of Intrinsic Disorder with Quality Assessment Using QUARTER

            Zhonghua Wu, Gang Hu, Christopher J. Oldfield, and Lukasz Kurgan

 

6. Modeling of Three-Dimensional RNA Structures Using SimRNA

            Tomasz K. Wirecki, Chandran Nithin, Sunandan Mukherjee, Janusz M. Bujnicki, and Michał J. Boniecki

 

7. Modeling Protein Homo-Oligomer Structures with GalaxyHomomer Web Server

            Minkyung Baek, Taeyong Park, Lim Heo, and Chaok Seok

 

8. Template-Based Modeling of Protein Complexes Using the PPI3D Web Server

            Justas Dapkūnas and Česlovas Venclovas

 

9. Protein-Protein and Protein-Peptide Docking with ClusPro Server

            Andrey Alekseenko, Mikhail Ignatov, George Jones, Maria Sabitova, and Dima Kozakov

 

10. Modeling of Protein Complexes and Molecular Assemblies with pyDock

            Mireia Rosell, Luis Angel Rodríguez-Lumbreras, and Juan Fernández-Recio

 

11. A Guide for Protein-Protein Docking Using SwarmDock

            Iain H. Moal, Raphael A.G. Chaleil, Mieczyslaw Torchala, and Paul A. Bates

 

12. Modeling Protein-Protein or Protein-DNA/RNA Complexes Using the HDOCK Webserver

            Yumeng Yan and Sheng-You Huang

 

13. IDP-LZerD: Software for Modeling Disordered Protein Interactions

            Charles Christoffer and Daisuke Kihara

 

14. AnAnaS: Software for Analytical Analysis of Symmetries in Protein Structures

            Guillaume Pagès and Sergei Grudinin

 

15. MDockPeP: A Webserver for Blind Prediction of Protein-Peptide Complex Structures

            Xianjin Xu and Xiaoqin Zou

 

16. Protocols for All-Atom Reconstruction and High-Resolution Refinement of Protein-Peptide Complex Structures

            Aleksandra Badaczewska-Dawid, Alisa Khramushin, Andrzej Kolinski, Ora Schueler-Furman, and Sebastian Kmiecik

 

17. DOCKGROUND Tool for Development and Benchmarking of Protein Docking Procedures

            Petras J. Kundrotas, Ian Kotthoff, Sherman W. Choi, Matthew M. Copeland, and Ilya A. Vakser

 

18. Molecular Dynamics Flexible Fitting: All You Want to Know about Resolution Exchange

            John W. Vant, Daipayan Sarkar, Chitrak Gupta, Mrinal S. Shekhar, Sumit Mittal, and Abhishek Singharoy

 

19. Protein Structure Modeling from Cryo-EM Map Using MAINMAST and MAINMAST-GUI Plugin

            Genki Terashi, Yuhong Zha, and Daisuke Kihara

 

20. Protocols for Fast Simulations of Protein Structure Flexibility Using CABS-Flex and SURPASS

            Aleksandra Badaczewska-Dawid, Andrzej Kolinski, and Sebastian Kmiecik

Blurb

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.