Repository Index

The official implementation of 3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction (ICLR 2023)

• ai-for-science
• diffusion-models
• drug-design
• equivariant-networks

Open Frontier Biomolecular Intelligence

Open source math and physics engine that executes MATLAB-syntax code. Features a modern compiler, automatic GPU acceleration for large calculations, and support for math on geometry / FEA calculations.

• matlab
• rust
• jit-compiler
• linear-algebra

MolTrans: Molecular Interaction Transformer for Drug Target Interaction Prediction (Bioinformatics)

Graph-based molecule modeling toolkit for cheminformatics

• cheminformatics
• molecular-modeling
• chemistry
• toolkit

Associated Repository for "Translation between Molecules and Natural Language"

A Python package for molecular docking with an extensive, highly-curated dataset and a set of realistic benchmark tasks for drug discovery.

Molecule Validation and Standardization

• rdkit
• python
• chemistry
• cheminformatics

Simple RDKit molecule editor GUI using PySide

LLM for Drug Editing, ICLR 2024

• chatgpt
• conversation
• drug
• drug-discovery

RTree2D is a 2D immutable R-tree for ultra-fast nearest and intersection queries in plane and spherical coordinates

• scala
• rtree
• 2d
• str

Auto-QChem is an automated workflow for the generation and storage of DFT calculations for organic molecules.

• cheminformatics
• dft-calculations
• automation
• feature

Accelerated tensor operations and dynamic neural networks based on reverse mode automatic differentiation for every device that can run Swift - from watchOS to Linux

• deep-learning
• deep-neural-networks
• gradient-descent
• automatic-differentiation

The Massively Parallel Quantum Chemistry program, MPQC, computes properties of atoms and molecules from first principles using the time independent Schrödinger equation.

Variations on Kirby & Paris' hydra battles and other entertaining math in Coq (collaborative, documented, includes exercises) [maintainer=@Casteran]

• coq
• hydra-battles
• ordinal-notations
• formal-proofs

Fast detection of repackaged Android applications based on the comparison of resource files included into the package.

• android
• android-security
• repackaging-detection
• java

CGRs, molecules and reactions manipulation

The d-SEAMS C++ core engine

• molecular-dynamics-simulation
• molecular-dynamics
• trajectory-analysis
• lua

ChemMine Tools: open source web framework for small molecule analysis

Multi-stage Riemannian flow matching for physically valid molecular docking, with GNINA scoring, PoseBusters filtering, CLI inference, and benchmarks.

• alphafold3
• docking
• drug-design
• drug-discovery

WebGL molecule viewer made with Babylon.js

Translatedfractional api base on golang . golang math tools fractional molecular denominator fraction calculation numerator denominator operations

• fractional
• molecular
• denominator
• operation

UV-first benchmark for protein-ligand docking with reproducible annotation, pocket similarity, and HPC workflows.

• benchmark
• bioinformatics
• cheminformatics
• computational-chemistry

Generative models for transcriptomic-driven or protein-driven molecular design (PaccMann^RL).

• deep-reinforcement-learning
• generative-model
• vae
• molecule-generation