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alf

Adaptive landscape flattening scripts for use with CHARMM/pyCHARMM Multi-site lambda dynamics

blade

BLaDE is a Basic Lambda Dynamics Engine for molecular dynamics based alchemical free energy calculations using multisite lambda dynamics on graphical processor units.

cdocker

crimm

directcouplinganalysis_pottsmodel_tensorflow

A Tensorflow implementation of Direct Coupling Analysis using Potts model

fastdock

FASTDock: A Pipeline for Allosteric Drug Discovery - example scripts and jupyter notebook

fastmbar

A fast solver for large scale MBAR/UWHAM equations

ml-matching

Machine Learning Approaching for Atom Typing.

msld-prep

A collection of python scripts and procedures to enable the building of ligands for Multi-site lambda Dynamics simulations using CHARMM/pyCHARMM

msld-workshop

Materials for five day workshop on using MSLD (including ALF and MSLD_py_prep) for drug discovery and protein engineering

pevae_paper

Deciphering protein evolution and fitness landscapes with latent space models

pycharmm-workshop

pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the University of Michigan by Charles Brooks' Group, June 20-24.

seq_struct_func

Example scripts for navigating protein sequence structure function space.