WEBnm@ v2.0: Web server and services for comparing protein flexibility.

ABSTRACT:

Background

Normal mode analysis (NMA) using elastic network models is a reliable and cost-effective computational method to characterise protein flexibility and by extension, their dynamics. Further insight into the dynamics-function relationship can be gained by comparing protein motions between protein homologs and functional classifications. This can be achieved by comparing normal modes obtained from sets of evolutionary related proteins.

Results

We have developed an automated tool for comparative NMA of a set of pre-aligned protein structures. The user can submit a sequence alignment in the FASTA format and the corresponding coordinate files in the Protein Data Bank (PDB) format. The computed normalised squared atomic fluctuations and atomic deformation energies of the

SUBMITTER: Tiwari SP 

PROVIDER: S-EPMC4339738 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature