This repository contains the source files and supplementary information for the the in silico-guided directed evolution of protease framework, which is described in Martin J. Thiele1§, Gaurao V. Dhoke1§, Felix Esser1, Isabell Hofmann1, Ulrich Schwaneberg1,2, Mehdi D. Davari*3, An In Silico-Guided Directed Evolution of Protease: Spotlighting the Beneficial Positions, To be published
The svl file contains the code nessasary to repliacte the docking results reported in the paper. It requires a mdb file (-rec) with receptors to which molecules in a second mdb (-lig) are docked.
-m determines how receptor side chains nearby the ligand are treated. ['Free', 'Fixed']
-k sets the strength of the pharmacophore constrains.
-p sets the maximum number of poses to retain.
-o Filename for the output mdb.
It features hardcoded pharmacophore constrains (lines 46-72) for the Subtilisin BL variant and the ligand Suc-AAPF-pNA used in the publication.
Contains the Subtilisin BL variants to which the ligand is docked (termed receptor in the svl), should be provided to the -rec option.
Contains a single Suc-AAPF-pNA molecule (refered to as ligand) which is docked to the receptors in SSM_v2.mdb, should be provided to the -lig option.
still missing