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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.
List of contents
Structural Modeling and Ligand Binding Prediction for Analysis of Structure-Unknown and Function-Unknown Proteins Using FORTE Alignment and PoSSuM Pocket Search.- The MULTICOM Protein Structure Prediction Server Empowered by Deep Learning and Contact Distance Prediction.- The Genome3D Consortium for Structural Annotations of Selected Model Organisms.- Estimating the Quality of 3D Protein Models Using the ModFOLD7 Server.- Prediction of Intrinsic Disorder with Quality Assessment Using QUARTER.- Modeling of Three-Dimensional RNA Structures Using SimRNA.- Modeling Protein Homo-Oligomer Structures with GalaxyHomomer Web Server.- Template-Based Modeling of Protein Complexes Using the PPI3D Web Server.- Protein-Protein and Protein-Peptide Docking with ClusPro Server.- Modeling of Protein Complexes and Molecular Assemblies with pyDock.- A Guide for Protein-Protein Docking Using SwarmDock.- Modeling Protein-Protein or Protein-DNA/RNA Complexes Using the HDOCK Webserver.- IDP-LZerD: Software for Modeling Disordered Protein Interactions.- AnAnaS: Software for Analytical Analysis of Symmetries in Protein Structures.- MDockPeP: A Webserver for Blind Prediction of Protein-Peptide Complex Structures.- Protocols for All-Atom Reconstruction and High-Resolution Refinement of Protein-Peptide Complex Structures.- DOCKGROUND Tool for Development and Benchmarking of Protein Docking Procedures.- Molecular Dynamics Flexible Fitting: All You Want to Know about Resolution Exchange.- Protein Structure Modeling from Cryo-EM Map Using MAINMAST and MAINMAST-GUI Plugin.- Protocols for Fast Simulations of Protein Structure Flexibility Using CABS-Flex and SURPASS.
