All Git Users → choderalab

15 open source projects by choderalab

[ Open user page on Github ]

1. Software Development

A primer on software development best practices for computational chemistry

✭ 159

python

2. Pymbar

Python implementation of the multistate Bennett acceptance ratio (MBAR)

✭ 109

python research

3. Yank

An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.

✭ 101

python molecular-dynamics

4. Ensembler

Automated omics-scale protein modeling and simulation setup.

✭ 38

python

5. Mmtools

Some collected tools for molecular simulation pipelines

✭ 22

python

6. gimlet

Graph Inference on MoLEcular Topology

✭ 24

python shell graph-theory tensorflow-gpu molecular-modeling

7. thermopyl

Tools for ThermoML parsing

✭ 15

python

8. protons

OpenMM testbed for constant-pH methodologies.

✭ 18

python simulation openmm constant-ph proton ph-methodologies

9. perses

Experiments with expanded ensembles to explore chemical space

✭ 99

python Jupyter Notebook TeX simulation molecular-dynamics openmm molecular-design free-energy-perturbation expanded-ensembles relative-free-energy

10. torsionfit

Bayesian tools for fitting molecular mechanics torsion parameters to quantum chemical data.

✭ 15

Rich Text Format python force-field bayesian-inference uncertainty-quantification forcefield torsions nsf-grant-che-1738979 forcefield-parameterization

11. espaloma

Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹https://arxiv.org/abs/2010.01196

✭ 105

python shell graph-learning forcefield-parameterization

12. neutromeratio

Tautomer ratios in solution

✭ 17

Jupyter Notebook python free-energy-calculations tautomer-ratios neural-net-potentials

13. qmlify

No description, website, or topics provided.

✭ 31

Jupyter Notebook python

14. pinot

Probabilistic Inference for NOvel Therapeutics

✭ 15

python TeX shell drug-discovery

15. openmm-tutorials

Quickstart Python tutorials helping molecular dynamics practitioners get up to speed with OpenMM

✭ 37

Jupyter Notebook jupyter-notebook molecular-dynamics openmm python-tutorial

1-15 of 15 user projects