Local Force Field Adjustment and Differential Analysis of Structure Mutations in iCn3d
Title: Local Force Field Adjustment and Differential Analysis of Structure Mutations in iCn3d
SNIC Project: SNIC 2022/22-771
Project Type: SNIC Small Compute
Principal Investigator: Marina Herrera Sarrias <marina.sarrias@math.su.se>
Affiliation: Stockholms universitet
Duration: 2022-08-17 – 2022-11-01
Classification: 10203
Homepage: https://github.com/hackathonismb/differential-analysis-of-residue-interactions-of-a-SNP-based-on-side-chain-prediction
Keywords:

Abstract

Cn3D is a web application to visualize and analyze structural data. One feature is to introduce mutations to the protein for comparison of the original structure and mutant variant. Currently, the structure is processed using scap, a program to predict side-chain conformations. However, no additional structural prediction for the mutation is done, such as how the backbone for the residue might change. This project seeks to offer additional improvements to the mutation structure estimation by predicting the conformational changes for the backbone and through MD simulations. The results are to be benchmarked by comparing the computationally predicted structures to experimentally derived structures (Dehouck et al., 2009; Dehouck et al., 2011). To aid in differential analysis, information on annotated functional regions of proteins from uniprot (UniProt Consortium 2021) and their distance to a mutation will also be provided as a new feature.