Visualization of protein sequence space with force-directed graphs, and their application to the choice of target-template pairs for homology modelling.

ABSTRACT: The protein sequence-structure gap results from the contrast between rapid, low-cost deep sequencing, and slow, expensive experimental structure determination techniques. Comparative homology modelling may have the potential to close this gap by predicting protein structure in target sequences using existing experimentally solved structures as templates. This paper presents the first use of force-directed graphs for the visualization of sequence space in two dimensions, and applies them to the choice of suitable RNA-dependent RNA polymerase (RdRP) target-template pairs within human-infective RNA virus genera. Measures of centrality in protein sequence space for each genus were also derived and used to identify centroid nearest-neighbour sequences (CNNs) potentially useful for production of

SUBMITTER: Mead DJT 

PROVIDER: S-EPMC7110651 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature