choderalab Goto Github PK

ring-open-fep

Ring-opening strategy for FEP.

rmsd-gradients

Fast gradients for receptor-ligand RMSD

rna-benchmark

RNA benchmarks associated with input coordinate files and experimental data

rna-bgsu-trinucleotide

RNA-BGSU trinucleotide dataset for QCArchive submission

rna-espaloma

Explore RNA systems with espaloma force field

rna_bgsu

Create RNA dataset for QCArchive Topics Resources

robots

Laboratory automation toolkits

rocsalt

Dual topology alchemical free energies

rumm

Recurrent Units-based Molecular Modeling

sake

Spatial Attention Kinetic Networks with E(n)-Equivariance

saltswap

Package to fluctuate the number of counterions in an OpenMM simulation

saltswap-results

Repository for the results of saltswap that are necessary for a first publication

sampl-r01

NIH NIGMS SAMPL R01 proposal

sampl4

Files for the SAMPL4 experiment

sampl5-experimental-logd-data

Experimental data for the SAMPL5 Cyclohexane/Water Log D challenge

sampl6-epik-jaguar-manuscript

Latex manuscript for the SAMPL6 epik and jaguar pKa paper

sampl6-logp-challenge-virtual-workshop

This repository contains slide decks of presentations that took place in SAMPL6 logP Challenge Virtual Workshop on May 16th, 2019.

sampl6-physicochemical-properties

SAMPL6 physicochemical property prediction challenge (logD, pKa and solubility)

sampl6-pka-challenge-manuscript

This repository contains the files for SAMPL6 pKa challenge overview manuscript.

sampl6-pka-measurements-manuscript

Repository for SAMPL6 pKa measurements manuscript.

sampl6-reference-epik-calculations-old

Reference pKa calculations for the SAMPL6 pKa challenge

sampl6-reference-pka-calculations

Reference pKa calculations for the SAMPL6 pKa challenge

sampl6_logp_ref_calc

Octanol-water logP predictions with YANK as reference calculations for SAMPL6 logP Challenge.

sams

Self-adjusted mixture sampling experiments

sams_dunbrack

This is a toolkit to estimate free energy differences between different Dunbrack clusters of kinase conformations using self-adjusted mixture sampling (SAMS).

selectivity

setd8-materials

Code and data for SETD8 simulations

simulation-health-reports

Notes for post-free-energy-calculation simulation health reports

single-molecule-splitting-probabilities

Computing single-molecule splitting probabilities as a test of reaction coordinate quality

smml

Exploring the interface between stat mech and machine learning - conference website