書籍「現場で活用するための生成AIエージェント実践入門」（講談社サイエンティフィック社）で利用されるソースコード

GPU-accelerated molecular docking software: Uni-Dock 2

Generate simple pharmacophore models from RDKit

PLACER is graph neural network for local prediction of protein-ligand conformational ensembles.

BitBIRCH-Lean, a memory-efficient implementation of BitBIRCH designed for high-throughput clustering of huge molecular libraries

BindCraft modified to make PyRosetta use and installation optional: no license needed

A toolkit developed to predict and analyze PROTAC-mediated ternary complexes using AlphaFold3 and Boltz-1.

Official inference framework for 1-bit LLMs

2025 RDKit UGM

Boltzina: Efficient and Accurate Virtual Screening via Docking-Guided Binding Prediction with Boltz-2

Source code for SMID calculation for paper

Docker Image for Redmine

Script for automatically submitting SLURM jobs, significantly simplifying routine calculations.

Python package to run molecular dynamics simulation of a protein-ligand complex in a single line of code.

[CVPR 25] MarkushGrapher: Joint Visual and Textual Recognition of Markush Structures

Vina-CUDA: further accelerating Autodock Vina with in-depth utilization of GPU hardware characteristics

SpaceHASTEN: A structure-based virtual screening tool for non-enumerated virtual chemical libraries

Python toolkit for pre- and post-processing of FMO calculations

Bluesky API documentation

[ICLR 2024] Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language Models

FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.

Benchmarking code accompanying the release of `bioemu`

DockCADD An automated computational framework for molecular docking