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analyze_exchanges

Replica Exchange Analysis

chacra

Reveal protein energy centers.

chem563

Statistical Mechanics Lecture Notes (Chem563 for Spring 2019)

creative_ml

Creative Machine Learning course and notebook tutorials in JAX, PyTorch and Numpy

eidos

computational biology tools

ensembler

Automated omics-scale protein modeling and simulation setup.

femto

A comprehensive toolkit for predicting free energies

getcontacts

Library for computing dynamic non-covalent contact networks in proteins throughout MD Simulation

gmxplumed

Dockerfile for Gromacs wih GPU support and PLUMED plugin.

md_scripts

Collection of example scripts for running and analyzing molecular dynamics

mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

molecular_dynamics_analysis_tools

Functions for lab-specific molecular dynamics analysis.

omm_hremd

openawsem

An implementation of the AWSEM coarse-grained protein folding forcefield in OpenMM

openmmtools

A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.

paramagpy

Calculating paramagnetic NMR effects in proteins

parmed

Parameter/topology editor and molecular simulator

prodar

Implementation of Protein Dynamically Activated Residues (ProDAR) for dyamics-informed protein function prediction/annotation

protein-transformer

Predicting protein structure through sequence modeling

pychesca

Chemical Shift Covariance Analysis with Python

rosetta-scripts

Some Rosetta Scripts that allow for various simple tasks

seq2ensemble

Seq2Ensemble: Collection of Colab based notebooks for facilitating conformational ensemble generation