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gromacs_py

Gromacs_py is a python library allowing a simplified use of the gromacs MD simulation software. Gromacs_py can build topologie based on a pdb file, create the simulation system (box, add water and ions) and run minimisation, equilibration and production run.

gromacs_ramd_portable_package

gromacs_scripts

assorted scripts for working with gromacs

gromit

Auxiliary tools for automated atomistic and coarse-grained molecular dynamics simulations using gromacs

grouppresentations

A collection of the group's presentations.

grover

This is a Pytorch implementation of the paper: Self-Supervised Graph Transformer on Large-Scale Molecular Data

groverfeat

An interface to the GROVER model for molecule featurization

gruenifai

Implementation grünif.ai: Interactive multi-parameter optimization of molecules in a continuous vector space

gryffin

gsalib

R package of utility functions for GATK

gseapy

Gene Set Enrichment Analysis in Python

gslnls

{gslnls}: GSL nonlinear least-squares fitting in R

gsvae

Variational AutoEncoder using Graph Scattering

gt4ireval

Generalizability Theory for Information Retrieval Evaluation

gt4sd-core

GT4SD, an open-source library to accelerate hypothesis generation in the scientific discovery process.

gta

Official code of Graph Truncated Attention for Retrosynthesis in AAAI2021

gtm

Guide Tree Merger

guacamol

Benchmarks for generative chemistry

guacamol-molecules

Lists of molecules for the GuacaMol objectives.

guacamol_baselines

Baselines models for GuacaMol benchmarks

guides

Tutorials for various workflows I've created e.g. homology modeling, score-based pharmacophore model classification.

gung-retrosynthesis-ancillary

Ancillary code to facilitate prediction of retrosynthesis reactions.

gvae4smiles

Grammar Variational Autoencoder for Smiles.

gvp-transformer

Implementation of the GVP-Transformer, which was used in the paper "Learning inverse folding from millions of predicted structures" for de novo protein design alongside Alphafold2

gym

A toolkit for developing and comparing reinforcement learning algorithms.

h-clmp

hackathon_2021_protein_stability

hacksig

A Tidy Framework to Hack Gene Expression Signatures

harmony

Fast, sensitive and accurate integration of single-cell data with Harmony

hat-reactivitypredictor

Demo of reactivity prediction of hydrogen atom transfer (HAT) reaction via machine learning