Fast design of arbitrary length loops in proteins using InteractiveRosetta.

ABSTRACT:

Background

With increasing interest in ab initio protein design, there is a desire to be able to fully explore the design space of insertions and deletions. Nature inserts and deletes residues to optimize energy and function, but allowing variable length indels in the context of an interactive protein design session presents challenges with regard to speed and accuracy.

Results

Here we present a new module (INDEL) for InteractiveRosetta which allows the user to specify a range of lengths for a desired indel, and which returns a set of low energy backbones in a matter of seconds. To make the loop search fast, loop anchor points are geometrically hashed using C α-C α and C β-C β distances, and the hash is mapped to start and end points in a pre-compiled random access file of n

SUBMITTER: Hooper WF 

PROVIDER: S-EPMC6154894 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature