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infiniteswitch

Implementation and testing of the infinite switch Hamiltonian exchange integrator.

integrator-benchmark

Code for enumerating and evaluating numerical methods for Langevin dynamics using near-equilibrium estimates of the KL-divergence. Accompanies https://doi.org/10.3390/e20050318

ir783-qsnap

Analysis of Quantitative Structure-Nanoparticle Assembly Prediction (QSNAP) descriptors for predicting drug-indocyanine dye (IR783) nanoparticle formation.

isothermal-titration-calorimetry

Contains code for generating and fitting data for isothermal titration calorimetry

kinase-metadynamics

To run metadynamics simulations using openMM (based on Peter Eastman's script)

learnreactions

Identify reaction events in reactive molecular dynamics simulations

levulinic-nanoreactor-qc

Data repository for: Application of the Ab Initio Nanoreactor to the Development of a New Peroxide-Driven Ketone Oxidation Reaction

libmolgrid

Comprehensive library for fast, GPU accelerated molecular gridding for deep learning workflows

ligan

Deep generative models for structure-based drug discovery

ligand-binding-pathsampling

Using path sampling to study ligand binding/unbinding kinetics

ligandr

Ligandr code

lime

Lime: Explaining the predictions of any machine learning classifier

liquidbenchmark

lomap

Alchemical mutation scoring map

mat

The official implementation of the Molecule Attention Transformer.

md-scripts

A collections of scripts for working molecular dynamics simulations

mdapackmol

MDAnalysis wrapper around Packmol

metk

Model Evaluation Toolkit

minidrugbank

A repository to track the creation and evolution of the MiniDrugBank Molecule set

mmtools

Some collected tools for molecular simulation pipelines

model_systems

Selection of model binding systems

molecular_rectifier

Given an RDKit molecule that does not sanitise, correct it until it does

molecules_dataset_collection

Collection of data sets of molecules for a validation of properties inference

moses

Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models

motor-thoughts

msm-pipeline

A pipeline for MSMs.

msmbuilder

:building_construction: Statistical models for biomolecular dynamics :building_construction:

msmexplorer

MSMExplorer is a visualization system for markov state models for protein folding networks

musashi

nano-drugbank

Cheminformatic analysis of small molecule type drugs in DrugBank for their ability to form nanoparticles with indocyanine dyes.