David Koes

rdkit-scripts. A collection of cheminformatics scripts that use rdkit

qsar-tools. Scripts for assisting in modeling quantitative structure activity relationships from 2D chemical data

md-scripts. A collections of scripts for working molecular dynamics simulations

pharmit. Open-source online virtual screening tools for large databases

show_contacts. PyMOL Plugin for displaying polar contacts

conformer_analysis. Jupyter Notebook

shapedb. C++

Open-Source-Molecular-Modelling. TeX

MD2NMR. NMR Chemical Shifts from Molecular Dynamics Simulation

slackfix. Hacks to make slack more usable

GNINA-1.0. Paper for release

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

ProDy. A Python Package for Protein Dynamics Analysis

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

notebooks. Jupyter Notebook

Pharmit-Interactive-Exploration-of-Chemical-Space. TeX

GLmol. A molecular viewer written in Javascript and WebGL

leadit. Under development

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

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

chai-lab. Chai-1, SOTA model for biomolecular structure prediction

slurm. Slurm: A Highly Scalable Workload Manager

open_combind. Open-source docking pipeline leveraging pairwise statistics

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

surfacemaker. JavaScript

gnina-celpp. Python

effortrack. Web interface for tracking effort on projects within a small to medium organization

asacalc. Solvent accessible surface area of PDB files

CommandLine2. This is a fork I made a long time ago of the LLVM commandline handling class since I liked it so much.