DEPECT

Design and Engineering of Proteins and Enzymes by Computational Tools

Introduction

Enzymes are key to bioindustry and some proteins are very important like COVID-19 neutralize antibody. However, it is hard to get efficient or useful biomacromolecules. Here I present DEPECT package for more easily and faster in silico design of biomacromolecules.

hybrid_redesign

Click the link to download the linux executable binary file of hybrid_redesign. It has been tested under Ubuntu 20.04.

To run hybrid_redesign scripts, make sure you have Rosetta, muscle and ncbi-blast+ suite installed!

usage:

./hybrid_redesign -s 4eb0.pdb -cid A -db /ndata/databases/blastdb/nr -ic 30 -e 1e-20 -sc 2 -nt 16 -m blast

After the calculation done(You can monitor it via top), run hrd.sh to generate combined hybrid_design.sc file.

enzde

combine autodock suites and modeller to design enzymes.

To run enzde scripts, make sure you have AutoDock suites and modeller installed!

• Install
  Edit the depect_enzde_config.py, change the ADT_PATH to where its installed.
• Demo
  ./demo.sh

Doc

mutfile format

12|LYS|A  
|  |   |  
|  |   |___Chain ID  
|  |___Mutate to which AA (Here is to mutate to a LYS)   
|___Residue Sequence Number in Pdb File   

cstfile format

CST_NAME:atom1,atom2
If the atom in the protein:
protein|chain id|number of residue|atom name
If the atom in the ligand:
ligand|atom number

in the zlj.cst used in demo:

distace1:protein|A|79|OG,ligand|13  

If the constraint is an angle, use 3 atoms, for a dihedral use 4 atoms.