CloudMol

Fold and design your protein with CloudMol on the cloud

Installation

pip install -U git+https://github.com/JinyuanSun/PymolFold.git

Usage

1. Protein Folding

from cloudmol.cloudmol import PymolFold
pf = PymolFold()         
pf.query_esmfold("MTYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE", '1pga')

2. Protein Design

pf.query_mpnn('./1pga.pdb')
# to fix some residues
# pf.query_mpnn('./1pga.pdb', fix_pos="1, 2, 3, 4, 5, 6, 7, 8, 9, 10")

the output is like:

>des_0,score=0.79912,seqid=0.6250
ATYTLNINGKTVKGTTTTTAANAAEAKKQFEAYVKSIGVNGTWTYDAATKTFTVTE
>des_1,score=0.75163,seqid=0.6071
ATYTLIINGKTVKGTTTVTAANAAEAQKQFTAYVKSKGVNGTWTYDASTKTFTVTE
>des_2,score=0.77783,seqid=0.5893
PTYTLNINGKTVKGTTTVTAADAATAKAQFDAYVKANGINGTWTFDASTKTFTVTE