dkoes
Removing barriers to computational drug discovery one bit at a time.
University of PittsburghPittsburgh
Pinned Repositories
conformer_analysis
GNINA-1.0
Paper for release
md-scripts
A collections of scripts for working molecular dynamics simulations
MD2NMR
NMR Chemical Shifts from Molecular Dynamics Simulation
Open-Source-Molecular-Modelling
qsar-tools
Scripts for assisting in modeling quantitative structure activity relationships from 2D chemical data
rdkit-scripts
A collection of cheminformatics scripts that use rdkit
shapedb
show_contacts
PyMOL Plugin for displaying polar contacts
slackfix
Hacks to make slack more usable
dkoes's Repositories
dkoes/rdkit-scripts
A collection of cheminformatics scripts that use rdkit
dkoes/qsar-tools
Scripts for assisting in modeling quantitative structure activity relationships from 2D chemical data
dkoes/md-scripts
A collections of scripts for working molecular dynamics simulations
dkoes/shapedb
dkoes/conformer_analysis
dkoes/slackfix
Hacks to make slack more usable
dkoes/GNINA-1.0
Paper for release
dkoes/MD2NMR
NMR Chemical Shifts from Molecular Dynamics Simulation
dkoes/pharmit
Open-source online virtual screening tools for large databases
dkoes/docs
Documentation for the Koes Research Group. Most likely woefully inadequate.
dkoes/ProDy
A Python Package for Protein Dynamics Analysis
dkoes/asker.js
A simple jquery plugin for asking a question and recording the answer
dkoes/leadit
Under development
dkoes/chai-lab
Chai-1, SOTA model for biomolecular structure prediction
dkoes/martinize.py
Create coarse grain Martini input files for Gromacs from (atomistic) pdb files.
dkoes/mmtf-pyspark
Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.
dkoes/open_combind
Open-source docking pipeline leveraging pairwise statistics
dkoes/openbabel
Open Babel is a chemical toolbox designed to speak the many languages of chemical data.
dkoes/3Dmol.js-Classroom-Response-System
dkoes/anitrain
scripts for training on ANI data
dkoes/cdnjs
The #1 free and open source CDN built to make life easier for developers.
dkoes/chap
CHAP is a tool for the functional annotation of ion channel structures:
dkoes/EquiBind
EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein
dkoes/iclr_2024
dkoes/liGAN
Deep generative models for structure-based drug discovery
dkoes/OpenChem
OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research
dkoes/openmm-setup
An application for configuring and running simulations with OpenMM
dkoes/rdkit
The official sources for the RDKit library
dkoes/sidechainnet
An all-atom protein structure dataset for machine learning.
dkoes/slurm
Slurm: A Highly Scalable Workload Manager