dkoes

David Koes's repositories

rdkit-scripts

A collection of cheminformatics scripts that use rdkit

Language:PythonMIT57 60

qsar-tools

Scripts for assisting in modeling quantitative structure activity relationships from 2D chemical data

Language:PythonApache-2.052 60

md-scripts

A collections of scripts for working molecular dynamics simulations

Language:PythonBSD-3-Clause34 5 3

show_contacts

PyMOL Plugin for displaying polar contacts

Language:PythonMIT15 2 2

shapedb

Language:C++NOASSERTION14 2 1

conformer_analysis

Language:Jupyter NotebookApache-2.013 20

GNINA-1.0

Paper for release

Language:Jupyter Notebook11 40

MD2NMR

NMR Chemical Shifts from Molecular Dynamics Simulation

Language:Jupyter NotebookBSD-3-Clause11 20

slackfix

Hacks to make slack more usable

Language:JavaScriptApache-2.01000

pharmit

Open-source online virtual screening tools for large databases

Language:HTMLApache-2.08 2 1

docs

Documentation for the Koes Research Group. Most likely woefully inadequate.

5 7 1

ProDy

A Python Package for Protein Dynamics Analysis

Language:PythonNOASSERTION4 20

asker.js

A simple jquery plugin for asking a question and recording the answer

Language:JavaScriptBSD-2-Clause3 20

leadit

Under development

Language:C++GPL-2.02 20

martinize.py

Create coarse grain Martini input files for Gromacs from (atomistic) pdb files.

Language:Python100

mmtf-pyspark

Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.

Language:PythonApache-2.01 10

open_combind

Open-source docking pipeline leveraging pairwise statistics

Language:PythonNOASSERTION100

openbabel

Open Babel is a chemical toolbox designed to speak the many languages of chemical data.

Language:C++GPL-2.01 20

3Dmol.js-Classroom-Response-System

Language:TeX020

anitrain

scripts for training on ANI data

Language:Python020

cdnjs

The #1 free and open source CDN built to make life easier for developers.

MIT010

chap

CHAP is a tool for the functional annotation of ion channel structures:

NOASSERTION000

EquiBind

EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein

MIT000

liGAN

Deep generative models for structure-based drug discovery

Language:PythonGPL-2.0000

OpenChem

OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research

Language:PythonMIT010

openmm-setup

An application for configuring and running simulations with OpenMM

NOASSERTION000

Pymol-script-repo

Collected scripts for Pymol

Language:Python000

rdkit

The official sources for the RDKit library

Language:HTMLBSD-3-Clause020

sidechainnet

An all-atom protein structure dataset for machine learning.

Language:PythonBSD-3-Clause010

slurm

Slurm: A Highly Scalable Workload Manager

Language:CNOASSERTION010