Principles of Protein Structure, Comparative Protein Modelling, and Visualisation
Part I: Introduction to Protein structure
- Chapter 1: Secondary Structure and Backbone Conformation
- Chapter 2: Super-secondary structure
- Chapter 3: Side Chain Conformation
- Chapter 4: Tertiary Protein Structure and folds
- SCOP and CATH: Short description of Fold Classification Servers
- Chapter 5: Quaternary Structure
Part II: Protein modelling with SWISS-MODEL
Please find here a (non exhaustive) list of other homology modelling tools and services
- HHpred: Server for homology detection and structure prediction by HMM-HMM comparison.
- I-Tasser: I-TASSER is a server for protein structure and function predictions. 3D models are built based on multiple-threading alignments by LOMETS and iterative TASSER assembly simulations.
- M4T: Comparative Modelling using a combination of multiple templates and iterative optimization of alternative alignments.
- Modeller: Software for homology or comparative modeling of protein three-dimensional structures. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints.
- ModWeb: A web server for automated comparative modeling that relies on PSI-BLAST, IMPALA and MODELLER.
- PHYRE2: A fold recognition server for predicting the structure and/or function of your protein sequence.
- RaptorX: RaptorX: a Web Portal for Protein Structure and Function Prediction.
Part III: Model quality
Model quality assessment tools are used to estimate the reliability of predicted protein structure models. The accuracy of individual models may vary significantly from the expected average quality due for instance to suboptimal target-template alignments, low template quality, structural flexibility or inaccuracies introduced by the modeling program. Individual assessment of each model is therefore essential. Please find here a (non exhaustive) list of tools and services:
- QMEAN: Server for model quality estimation.
- ModEval: Model Evaluation Server, an evaluation tool for protein structure models.
- ModFOLD: Model Quality Assessment Server.
- ProQ2: A neural network based predictor based on a number of structural features, which predicts the quality of different parts of protein model.
- SAVES: The Structure Analysis and Verification Server, runs up to six different programs for structure validation.
Part IV: Protein Structure Visualization
The following tools allow visualization of macromolecular structures in PDB format (i.e. experimental structures and models). SWISS-MODEL results are best viewed and manipulated with the program DeepView (Swiss-PdbViewer), which also allows to modify the target template alignment for the SWISS-MODEL "project mode".
- DeepView/Swiss-PdbViewer: Software for protein structure analysis and visualization.
- Jmol: an open-source Java viewer for chemical structures in 3D.
- MolScript: A program for displaying molecular 3D structures.
- OpenStructure: Open-Source Computational Structural Biology Framework.
- POV-Ray: Open Source Raytracing software.
- PyMol: A Python based open-source viewer for visualization of macromolecular structures.
- UCSF Chimera: An extensible program for interactive visualization and analysis of molecular structures.
- VMD: VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
- Appendix A: Recommended reading