Includes: Homology Modelling, Loop Refinement of predicted model, Model analysis for quality assessment
Tools: Prime Homology Modelling and Refinement, Ramachandran plot, Protein Report, Maestro
Audience level: Beginners - Intermediate
There are often instances in Structural Biology (SB) modelling where the initial target has not been crystalised for various reasons, but the aim is to pursue some kind of SB program. In this workshop we explore useful techniques to predict a structure for our starting target protein, using a single template 1VPE and predict the structure of a Phosphoglycerate Kinase. This exercise explores the full use of the Homology Modelling interface from using BLAST to search for homologues to the initial FASTA sequence through to aligning and editing sequences in different ways. Finally the model is built using libraries of sidechains and backbones, and refined using physics-based criteria which are discussed in terms of the variable dielectric model VSGB2.0 and the hydrophobic-packing terms in the loop prediction algorithm. The quality of the predicted model is assessed using a Ramachandran plot and protein report tools.
This example has been extracted from the Quick Start Guide which is part of the installed documentation. After this workshop, users can easily refer to the documentation to further their knowledge in building homo- and hetero-multimers for which there are worked-up examples to follow.