An automated protocol for modelling peptide substrates to proteases.

ABSTRACT:

Background

Proteases are key drivers in many biological processes, in part due to their specificity towards their substrates. However, depending on the family and molecular function, they can also display substrate promiscuity which can also be essential. Databases compiling specificity matrices derived from experimental assays have provided valuable insights into protease substrate recognition. Despite this, there are still gaps in our knowledge of the structural determinants. Here, we compile a set of protease crystal structures with bound peptide-like ligands to create a protocol for modelling substrates bound to protease structures, and for studying observables associated to the binding recognition.

Results

As an application, we modelled a subset of protease-peptide comp

SUBMITTER: Ochoa R 

PROVIDER: S-EPMC7771086 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature