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leelasd / Taka_ConstrainedEmbedding.ipynb
Created October 27, 2020 22:54 — forked from greglandrum/Taka_ConstrainedEmbedding.ipynb
Taka_ConstrainedEmbedding.ipynb
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leelasd / Schmidtke_ReversingReactions.ipynb
Created October 27, 2020 22:52 — forked from greglandrum/Schmidtke_ReversingReactions.ipynb
Schmidtke_ReversingReactions.ipynb
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leelasd / SAR Tables.ipynb
Created October 27, 2020 22:51 — forked from greglandrum/SAR Tables.ipynb
SAR Tables.ipynb
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leelasd / 3D-MCS.ipynb
Created October 27, 2020 22:51 — forked from greglandrum/3D-MCS.ipynb
3D-MCS.ipynb
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leelasd / hydrophobic_moment.py
Created September 30, 2020 18:26 — forked from JoaoRodrigues/hydrophobic_moment.md
Peptide/Protein Hydrophobic Moment Calculator
#!/usr/bin/env python
"""
Calculates a set of properties from a protein sequence:
- hydrophobicity (according to a particular scale)
- mean hydrophobic dipole moment assuming it is an alpha-helix.
- total charge (at pH 7.4)
- amino acid composition
- discimination factor according to Rob Keller (IJMS, 2011)
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leelasd / bio_align.py
Created September 30, 2020 18:25 — forked from JoaoRodrigues/bio_align.py
Sequence-based structure alignment of protein structures with Biopython
#!/usr/bin/env python
"""Sequence-based structural alignment of two proteins."""
import argparse
import pathlib
from Bio.PDB import FastMMCIFParser, MMCIFIO, PDBParser, PDBIO, Superimposer
from Bio.PDB.Polypeptide import is_aa
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leelasd / run_md.py
Created August 10, 2020 20:44 — forked from dwhswenson/run_md.py
Simple OpenMM-based MD from Gromacs files
#!/usr/bin/env python
# coding: utf-8
##########################################################################
# this script was generated by openmm-builder. to customize it further,
# you can save the file to disk and edit it with your favorite editor.
##########################################################################
# REQUIRES:
# * OpenMM (core dynamics)
@leelasd
leelasd / run_pdbfixer.sh
Created August 2, 2020 15:09
PDB Fixer script from openmmforcefields
#!/bin/bash -x
# This script is for running the preparation workflow to create a pdb file that is compatible for parsing by openmm
# It reads in a pdb provided in the supplementary information from 10.1021/ja512751q always of the form:
# {target}_protein.pdb and runs pdb4amber and pdbfixer to generate a new pdb file with form {target}_protein_fixed.pdb
if [ $1 == "-h" ]; then
echo "
This script assumes that the first argument is an unprocessed pdb file of the form
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