Protein Structure Prediction

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

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

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

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

Chapter 5 Prediction of Intrinsic Disorder with Quality Assessment Using QUARTER

Chapter 6 Modeling of Three-Dimensional RNA Structures Using SimRNA

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

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

Chapter 9 Protein–Protein and Protein–Peptide Docking with ClusPro Server

Chapter 10 Modeling of Protein Complexes and Molecular Assemblies with pyDock

Chapter 11 A Guide for Protein–Protein Docking Using SwarmDock

Chapter 12 Modeling Protein–Protein or Protein–DNA/RNA Complexes Using the HDOCK Webserver

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

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

Chapter 15 MDockPeP: A Web Server for Blind Prediction of Protein–Peptide Complex Structures

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

Chapter 17 Dockground Tool for Development and Benchmarking of Protein Docking Procedures

Chapter 18 Molecular Dynamics Flexible Fitting: All You Want to Know About Resolution Exchange

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

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