jchodera Goto Github PK

error-analysis-notebooks

Error analysis notebooks

examol

Strategies for sampling over chemical space

experiments-binding-affinity

fah-viewer

Folding@home 3D Viewer

fah_prep

suite of functions to prepare simulations (docking, free energy) for use with folding at home.

fahmunge

Tools for Munging Folding@Home datasets

fragmenter-manuscript

freeenergyframework

Package for consistent reporting of relative free energy results

freesolv

Experimental and Calculated Small Molecule Hydration Free Energies

gbff

Tools for Bayesian forcefield development

genome-read-comparison

Comparison of genome reads

goodiebag

itc-worksheet

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

itctools

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

jacs-dataset-analysis

Re-analysis of the Schrödinger JACS dataset

jdcthesis

John Chodera's PhD thesis latex source

kinase-benchmark

Benchmark Yank against kinases and FDA approved inhibitors.

kinase-ecoli-expression-panel

Selection of kinase constructs suitable for E coli expression

kinodata

Collection of scripts / notebooks to reliably select datasets

kinoml

Structure-informed machine learning for kinase modeling

lab-protocols

A collection of protocols, primarily for automated protein expression and mutagenesis

latex-cv

Example showing how LaTeX can be used to produce a nice-looking curriculum vitae (CV).

latex-manuscript-template

Simple LaTeX manuscript template

ligand-binding-pathsampling

Using path sampling to study ligand binding/unbinding kinetics

liquidbenchmark

livecomsjournal.github.io

GitHub Pages site for the Living Journal of Computational Molecular Science

maxentile-notebooks

Miscellaneous preliminary notebooks

mcce

Multi-Conformation Continuum Electrostatics

mcce-charges

generating ligand charges

mdtraj

A modern, open library for the analysis of molecular dynamics trajectories