Dan-Burns's repositories
Analyze_Exchanges
Replica Exchange Analysis
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.
openmmtools
A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
paramagpy
Calculating paramagnetic NMR effects in proteins
Seq2Ensemble
Seq2Ensemble: Collection of Colab based notebooks for facilitating conformational ensemble generation
openawsem
An implementation of the AWSEM coarse-grained protein folding forcefield in OpenMM
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
rosetta-scripts
Some Rosetta Scripts that allow for various simple tasks