choderalab Goto Github PK

importance-of-shadow-work

Investigating the error introduced by neglecting shadow work

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.

itc-worksheet

A simple approach to achieving high accuracy in isothermal titration calorimetry (ITC) measurements

itc_experiment_notebook

Records of ITC Experiments

itctools

Tools for setting up ITC experiments in an automated fashion using the Tecan EVO and Auto-iTC 200.

jager

kaizen

Continual improvement

kinalysis

Scripts for analyzing simulations of kinases!

kinase-benchmark

Benchmark Yank against kinases and FDA approved inhibitors.

kinase-ecoli-expression-panel

Selection of kinase constructs suitable for E coli expression

kinase-metadynamics

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

kinase-modeller

kinase-resistance-mutants

kinomedb-webclient

klogw

Molecular simulation algorithms and computational statistics blog

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

metk

Model Evaluation Toolkit

mhc

Examples for MHC-peptide free energy calculations using YANK

mltl

Machine learning of thermodynamic lengths

mmtools

Some collected tools for molecular simulation pipelines