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afes-openmm-atom-1

OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method

asitedesign

automd

Easy to get started with molecular dynamics simulation.

backup-slack

A script for backing up your message history from Slack

bat.py

The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy calculations on protein-ligand systems, compatible with the AMBER and OpenMM simulation packages.

blade

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

cappable-seq

compare-annotations

A script for comparing old vs new versions of genome annotations

convert-namd-coordinates-and-amber-parameters-to-desmond-cms

Use these files to convert Amber parameter file + NAMD simulation output file > desmond .cms file

createremddirs

Automatically generate input for running M-REMD simulations (and more) in Amber.

desres-ff

Force Fields

dimple

Coyote-Maestas Final Version

ecoli_promoter_mpra

evolved_synthetic_auxotrophs

fep-restraints

Tools to add restraints to FEP runs (currently only AB-FEP). Includes a workflow to determine reference structures and restraint widths from plain MD simulations.

force-fields

Force Fields

genome_recoding

iqmol3

IQmol version 3

md-simulation

A Generalised workflow for obtaining protein and peptide molecular structures, docking the peptide into the protein and running a molecular dynamic simulation over a large number of trajectories.

mdfit

Automated molecular dynamics simulations workflow for high-throughput assessment of protein-ligand dynamics

mutation_maker

Application for mutagenic primer design. Facilitates development of biocatalysts (Green Chemistry) and new therapeutic proteins.

openmm_sdm_workflow

Example of the use of the single-decoupling method setup workflow

oscar

postdoc-funding-schemes

Funding schemes and travel grant opportunities for postdocs

pseudocycle_small_molecule_binder

Small_molecule_binder_design_use_pseudocycles

pssm_promoter_tool

puffin

deep learning-inspired explainable sequence model for transcription initiation

puffin_manuscript

qmhub

A QM/MM interface

recoli57

Supporting code for Ostrov et al., Science, 2016