Design and Engineering of Proteins and Enzymes by Computational Tools
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.
Click the link to download the linux executable binary file of hybrid_redesign. It has been tested under Ubuntu 20.04.
./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.
combine autodock suites and modeller to design enzymes.
- Install
Edit the depect_enzde_config.py, change the ADT_PATH to where its installed. - Demo
./demo.sh
12|LYS|A
| | |
| | |___Chain ID
| |___Mutate to which AA (Here is to mutate to a LYS)
|___Residue Sequence Number in Pdb File
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.