1.deepchem / deepchem
Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology
- drug-discovery
- quantum-chemistry
- deep-learning
- biology
- materials-science
- hacktoberfest
+446 stars
from 6,677 · score 6.10
Trending repositories
Ranked by Attention Score: stars gained over the last 180 complete days
37 repositories by Attention Score · May 9, 2026 – Nov 4, 2026 (UTC)
2.jwohlwend / boltz
Official repository for the Boltz biomolecular interaction models
- binding-prediction
- drug-discovery
- protein-structure
+373 stars
from 3,919 · score 5.92
+259 stars
from 3,407 · score 5.56
4.lammps / lammps
Public development project of the LAMMPS MD software package
- molecular-dynamics
- lammps
- simulation
- kokkos
+254 stars
from 2,868 · score 5.54
5.chemprop / chemprop
Message Passing Neural Networks for Molecule Property Prediction
- machine-learning
- chemistry
- neural-networks
- drug-discovery
+175 stars
from 2,341 · score 5.17
6.gcorso / DiffDock
Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
- diffusion-models
- docking
- binding
- computational-biology
- equivariance
- machine-learning
- +2 more
+102 stars
from 1,497 · score 4.63
7.openbabel / openbabel
Open Babel is a chemical toolbox designed to speak the many languages of chemical data.
- chemistry
- chemical-data
- cheminformatics
- c-plus-plus
- chemical-toolbox
+99 stars
from 1,306 · score 4.61
8.deepmodeling / Uni-Mol
Official Repository for the Uni-Mol Series Methods
- molecular-modeling
- pre-trained-model
- pretraining
- deep-learning
+87 stars
from 1,088 · score 4.48
9.3dmol / 3Dmol.js
WebGL accelerated JavaScript molecular graphics library
- molecular-graphics
- molecular-modeling
- computational-biology
- computational-chemistry
+72 stars
from 964 · score 4.29
10.gromacs / gromacs
Public/backup repository of the GROMACS molecular simulation toolkit. Please do not mine the metadata blindly; we use https://gitlab.com/gromacs/gromacs for code review and issue tracking.
+71 stars
from 903 · score 4.28
11.psi4 / psi4
Open-Source Quantum Chemistry – an electronic structure package in C++ driven by Python
- quantum-chemistry
- c-plus-plus
- python
- computational-chemistry
- chemistry
- physics
+67 stars
from 1,168 · score 4.22
12.kexinhuang12345 / DeepPurpose
A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)
- drug-repurposing
- deep-learning
- drug-target-interactions
- toolkit
- covid19
- virtual-screening
- +13 more
+49 stars
from 1,152 · score 3.91
13.arneschneuing / DiffSBDD
A Euclidean diffusion model for structure-based drug design.
- ddpm
- drug-design
- equivariance
- generative-model
- graph-neural-networks
- machine-learning
+38 stars
from 499 · score 3.66
14.molecularsets / moses
Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models
- machine-learning
- generative-models
- drug-discovery
- benchmark
+33 stars
from 963 · score 3.53
15.cdk / cdk
The Chemistry Development Kit
- code4lib
- chemistry
- java
- cheminformatics
- bioinformatics
- blueobelisk
+33 stars
from 579 · score 3.53
16.mdtraj / mdtraj
An open library for the analysis of molecular dynamics trajectories
- molecular-dynamics
- python
- mdtraj
- rmsd
- dihedral-angles
- pdb
- +2 more
+30 stars
from 713 · score 3.43
17.cclib / cclib
Parsers and algorithms for computational chemistry logfiles
- python
- computational-chemistry
- quantum-chemistry
+29 stars
from 404 · score 3.40
18.Mariewelt / OpenChem
OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research
- computational-chemistry
- computational-biology
- deep-learning
- deep-neural-networks
- graph-convolutional-networks
- drug-discovery
- +5 more
+25 stars
from 735 · score 3.26
19.datamol-io / datamol
Molecular Processing Made Easy.
- python
- molecule
- rdkit
- drug-discovery
- drug-design
- molecules
- +2 more
+25 stars
from 531 · score 3.26
20.epam / Indigo
Universal cheminformatics toolkit, utilities and database search tools
- indigo
- bingo
- cheminformatics
- chemistry
- python
- dotnet
- +9 more
+25 stars
from 389 · score 3.26
+23 stars
from 515 · score 3.18
22.chainer / chainer-chemistry
Chainer Chemistry: A Library for Deep Learning in Biology and Chemistry
- deep-learning
- chemistry
- neural-network
- biology
- chainer
- python
- +1 more
+22 stars
from 693 · score 3.14
23.bjodah / chempy
⚗ A package useful for chemistry written in Python
- chemistry
- physical-chemistry
- chemical-kinetics
- chemical-formulas
- chemical-reaction-model
- python
- +1 more
+21 stars
from 638 · score 3.09
24.mordred-descriptor / mordred
a molecular descriptor calculator
+17 stars
from 469 · score 2.89
25.guanjq / targetdiff
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
- iclr2023
+16 stars
from 335 · score 2.83
26.thinng / GraphDTA
GraphDTA: Predicting drug-target binding affinity with graph neural networks
+16 stars
from 295 · score 2.83
27.AstraZeneca / chemicalx
A PyTorch and TorchDrug based deep learning library for drug pair scoring. (KDD 2022)
- deep-learning
- pytorch
- deep-chemistry
- graph-neural-network
- drug
- drug-pair
- +13 more
+13 stars
from 775 · score 2.64
28.wengong-jin / icml18-jtnn
Junction Tree Variational Autoencoder for Molecular Graph Generation (ICML 2018)
+13 stars
from 551 · score 2.64
29.hkmztrk / DeepDTA
Source code for "DeepDTA: deep drug-target binding affinity prediction"
- protein-ligand-interactions
- convolutional-neural-networks
+12 stars
from 297 · score 2.56
30.seyonechithrananda / bert-loves-chemistry
bert-loves-chemistry: a repository of HuggingFace models applied on chemical SMILES data for drug design, chemical modelling, etc.
- huggingface
- bert
- chemical-modelling
- chemical-smiles-data
+11 stars
from 491 · score 2.48
+11 stars
from 240 · score 2.48
32.awslabs / dgl-lifesci
Python package for graph neural networks in chemistry and biology
- deep-learning
- graph-neural-networks
- dgl
- cheminformatics
- bioinformatics
- geometric-deep-learning
- +2 more
+10 stars
from 801 · score 2.40
33.pschwllr / MolecularTransformer
The repository host gives no description.
+8 stars
from 421 · score 2.20
34.MolecularAI / ReinventArchived
The repository host gives no description.
- cheminformatics
- neural-networks
- astrazeneca
- reinforcement-learning
- denovo-design
- transfer-learning
+7 stars
from 371 · score 2.08
35.isayev / ReLeaSE
Deep Reinforcement Learning for de-novo Drug Design
- deeplearning
- reinforcement-learning
- cheminformatics
- molecular-modeling
- drug-discovery
- qsar
+7 stars
from 368 · score 2.08
36.samoturk / mol2vecArchived
Mol2vec - an unsupervised machine learning approach to learn vector representations of molecular substructures
- python
- machine-learning
- cheminformatics
+7 stars
from 287 · score 2.08
37.bp-kelley / descriptastorus
Descriptor computation(chemistry) and (optional) storage for machine learning
+5 stars
from 277 · score 1.79