Arthur Zalevsky aozalevsky

## alphafold_multifragment_file.py
import prody

# Set fname
fname = 'AF-Q96M86-F13-model_v1.cif.gz'

# Use prody to parse AlphaFold structure in mmCIF format
pdb, header = prody.parseMMCIF(fname, header=True)

# extract coordinates of the fragment in the reference sequence
# e.g. Uniprot AC Q96M86

## alphafold_plddt2pdb.py
import prody
import dill  # or pickle

# Read AF2 output
with open('result_model_1.pkl', 'rb') as f:
    af = dill.load(f)

# Parse PDB structure
pdb = prody.parsePDB('relaxed_model_1.pdb')

## protein_geodesic_distance.ipynb

      
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                aozalevsky
                / protein_geodesic_distance.ipynb
            
            
              Last active
              June 3, 2022 14:05
            
              
                Calculate geodesic distance on the protein surface
              
          
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## Singularity.def
Bootstrap: docker
From: ubuntu:22.04
Stage: spython-base

%labels

    MAINTAINER Arthur Zalevsky <aozalevsky@gmail.com>

%post
	import prody

	# Set fname
	fname = 'AF-Q96M86-F13-model_v1.cif.gz'

	# Use prody to parse AlphaFold structure in mmCIF format
	pdb, header = prody.parseMMCIF(fname, header=True)

	# extract coordinates of the fragment in the reference sequence
	# e.g. Uniprot AC Q96M86
	import prody
	import dill # or pickle

	# Read AF2 output
	with open('result_model_1.pkl', 'rb') as f:
	af = dill.load(f)

	# Parse PDB structure
	pdb = prody.parsePDB('relaxed_model_1.pdb')
	Bootstrap: docker
	From: ubuntu:22.04
	Stage: spython-base

	%labels

	MAINTAINER Arthur Zalevsky <aozalevsky@gmail.com>

	%post