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covid

MolSSI SARS-CoV-2 Biomolecular Simulation Data and Algorithm Store

covid-moonshot

Scripts and input files associated with docking and free energy calculations for the COVID Moonshot

covid-moonshot-manuscript

Scripts, figures, and data relevant to the COVID moonshot manuscript

covid-moonshot-ml

Scripts and models for ML with COVID Moonshot data.

cpdetect

Change Point detection

cragganmore

Cytochrome P450 YANK calculations

cup-xiv

Slides, iPython notebooks, and references for CUP XIV presentation.

cyp450-affinity

Experimental affinity data regarding Cytochrome P450 BM3 model system is organized under this repository.

ddr1_and_kinase_promiscuity_materials

Code and data for the paper 'What makes a kinase promiscuous for inhibitors?'.

density

density-measurements

Density measurements made with the Chodera lab Mettler-Toledo DM40 and SC30 sample changer

dispensing-errors-manuscript

IPython notebook to accompany dispensing errors manuscript

docker-fah-client

Information on running the Folding@Home client inside a docker image

drylab-protocols

A set of standard tools for setting proteins and small molecules for molecular simulations.

duke-cbb-talk-2014-10-06

Slides from John Chodera's CBB talk at Duke University on 6 Oct 2014

dunbrack_assignment

Scripts to assign conformation(s) to Dunbrack DFG clusters [Modi and Dunbrack, 2019].

enhanced-sampling-tmem175

Repository for running and assessing enhanced sampling simulations of TMEM175

ensembler

Automated omics-scale protein modeling and simulation setup.

ensembler-manuscripts

Manuscript for Ensembler v1

ensembler2

epik-ligands

This repository contains ligands parametrized for MCCE using Epik to predict protonation states and OpenEye for charge assignment.

erk-ancestral-materials

ERK ancestral reconstruction

erlangen-2014

Talk slides for Erlangen 2014 Molecular Modelling workshop.

espaloma

Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹https://arxiv.org/abs/2010.01196

espaloma_charge

Standalone charge assignment from Espaloma framework.

espalomax

Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹https://arxiv.org/abs/2010.01196

examol

Strategies for sampling over chemical space

expressionexplorer

fah-open-datasets

Open datasets generated by Folding@Home and curated by the Chodera Lab

fah-public-data

Tools and documentation for uploading open data to AWS Public Datasets