iwatobipen

h2o-llmstudio

H2O LLM Studio - a framework and no-code GUI for fine-tuning LLMs. Documentation: https://docs.h2o.ai/h2o-llmstudio/

plotters

A rust drawing library for high quality data plotting for both WASM and native, statically and realtimely 🦀 📈🚀

REINVENT4

AI molecular design tool for de novo design, scaffold hopping, R-group replacement, linker design and molecule optimization.

brename

A practical cross-platform command-line tool for safely batch renaming files/directories via regular expression

posebusters

Plausibility checks for generated molecule poses.

Uni-Dock

Uni-Dock: a GPU-accelerated molecular docking program

ChEMBL_Structure_Pipeline

ChEMBL database structure pipelines

GromacsWrapper

GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).

molpal

active learning for accelerated high-throughput virtual screening

IgLM

Generative Language Modeling for Antibody Design

scikit-mol

scikit-learn classes for molecular vectorization using RDKit

molskill

Extracting medicinal chemistry intuition via preference machine learning

tblite

Light-weight tight-binding framework

Uni-GBSA

An automatic workflow to perform MM/GB(PB)SA calculations from force field building, and structure optimization to free energy calculation.

rxdock

RxDock is a fork of rDock. Note: the latest code is under development. Please do git checkout patched-rdock after clone if you want patched rDock. [IMPORTANT NOTE: pull requests should be posted on GitLab, this is a read-only source code mirror]

lightweight-registration

alphafold2rave

protocolGromacs

Automatic gromacs protocol from preparation to production with ligand parametrization through

lig3dlens

DSDP

Deep Site and Docking Pose (DSDP) is a blind docking strategy accelerated by GPUs, developed by Gao Group. For the site prediction part, several modifications are introduced to PUResNet program. The pose sampling part is similar as AutoDock Vina combined with a number of modifications.

DeepPROTACs

DeepDockingGUI

ccpbiosim-2023

Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week

RLDOCK

reeds

This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration free energies or ligand binding free energies.

SeparatedTopologies

Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).

EDTSurf

mirror of https://zhanglab.ccmb.med.umich.edu/EDTSurf/

scipion-chem

Base Scipion plugin defining objects and protocols for CHEMoinformatics

openmm_benchmark

OpenMM benchmark Repo

DiffDock

Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking