choderalab Goto Github PK

kinomedb-webclient

klogw

Molecular simulation algorithms and computational statistics blog

knowledge-base

A repository for Chodera Lab members to get up to speed on the foundational knowledge necessary for getting the most out of the lab!

latex-manuscript-template

Simple LaTeX manuscript template

ldha-mcce

MCCE2 calculations for Lactate dehydrogenase A (collaboration with Thompson lab and Gunner lab)

ligand-binding-pathsampling

Using path sampling to study ligand binding/unbinding kinetics

ligandr

Ligandr code

liquid-handling-tester

Repository for development of two dye based liquid handler testing system.

liquidbenchmark

malt

Molecular Active Learning Testbed

mcce-charges

generating ligand charges

mcce-structures

men1

Computational prediction of the impact of point mutations on MEN1 inhibitor binding.

metk

Model Evaluation Toolkit

mhc

Examples for MHC-peptide free energy calculations using YANK

missense-kinase-toolkit

An ETL pipeline package to facilitate structure-based ML for missense human kinase property prediction

mltl

Machine learning of thermodynamic lengths

mmtools

Some collected tools for molecular simulation pipelines

model_systems

Selection of model binding systems

modelforge

Infrastructure to implement and train NNPs

moldr

Manifold optimization for linear dimensionality reduction of MD trajectories

mpiplus

Utilities to run on MPI.

msm-mfpt

Evaluating MSM-estimated mean first passage times

msm-pipeline

A pipeline for MSMs.

msms

Markov state models

mtenn

Modular Training and Evaluation of Neural Networks

musashi

mutation-analysis

Visualisation methods to analyse protein mutational landscapes

nano-drugbank

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

nanoparticles

Scripts to set-up and run simulations composed of mixtures of insoluble molecules and dye.