Brooks Group at the University of Michigan

Brooks Group at the University of Michigan's repositories

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.

Language:Jupyter NotebookMIT5500

FastMBAR

A fast solver for large scale MBAR/UWHAM equations

Language:PythonMIT32 4 2

PEVAE_Paper

Deciphering protein evolution and fitness landscapes with latent space models

Language:PythonGPL-3.030 5 5

FASTDock

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

Language:Rich Text FormatMIT19 4 1

DirectCouplingAnalysis_PottsModel_Tensorflow

A Tensorflow implementation of Direct Coupling Analysis using Potts model

Language:Python1000

MSLD-Workshop

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

Language:Rich Text FormatMIT8 50

crimm

Language:Rich Text FormatGPL-3.0300

seq_struct_func

Example scripts for navigating protein sequence structure function space.

Language:Jupyter NotebookMIT3 20

ML-Matching

Machine Learning Approaching for Atom Typing.

Language:Python200

msld-prep

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

Language:ShellGPL-3.0100

ALF

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

Language:ShellGPL-3.0000

anc_acyl

Language:Rich Text Format000

Ancestral_AT_paper

Language:Jupyter Notebook000

BLaDE

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

Language:ShellGPL-3.0000

CDOCKER

Language:Cuda000