Software Ecosystems
Complete software stacks organized by scientific domain.
Chemistry & Cheminformatics
Core Stack
| Tool | Purpose | Link |
|---|---|---|
| RDKit | Cheminformatics foundation | rdkit.org |
| OpenBabel | Format conversion | openbabel.org |
| Datamol | RDKit for data science | datamol.io |
Deep Learning
| Tool | Purpose | Link |
|---|---|---|
| DeepChem | ML for chemistry | deepchem.io |
| Chemprop | Message passing NNs | github |
| DGL-LifeSci | GNNs for life science | github |
Materials Science
Core Stack
| Tool | Purpose | Link |
|---|---|---|
| pymatgen | Materials analysis | pymatgen.org |
| matminer | Feature engineering | hackingmaterials.lbl.gov/matminer |
| ASE | Atomistic simulations | wiki.fysik.dtu.dk/ase |
| JARVIS | Integrated workflows | jarvis.nist.gov |
Neural Network Potentials
| Tool | Purpose | Link |
|---|---|---|
| MACE | Equivariant NNPs | github |
| NequIP | E(3)-equivariant NNPs | github |
Biology & Drug Discovery
| Tool | Purpose | Link |
|---|---|---|
| DeepChem | Drug discovery ML | deepchem.io |
| BioPython | Sequence analysis | biopython.org |
| PyMOL | Molecular visualization | pymol.org |
Installation Recipes
Chemistry Environment
conda create -n chem python=3.10
conda activate chem
conda install -c conda-forge rdkit
pip install datamol deepchem jupyterMaterials Environment
conda create -n materials python=3.10
conda activate materials
pip install pymatgen matminer ase jupyterFull Stack
conda create -n ai4science python=3.10
conda activate ai4science
conda install -c conda-forge rdkit
pip install pymatgen matminer deepchem jupyter pandas scikit-learn torchAwesome Lists
Curated resource collections for finding more tools and papers.
General
| List | Focus |
|---|---|
| awesome-ai-for-science | AI tools for scientific research |
Chemistry & Drug Discovery
| List | Focus |
|---|---|
| awesome-cheminformatics | Cheminformatics tools |
| awesome-python-chemistry | Python chemistry tools |
| awesome-chemistry-datasets | ML datasets |
| awesome-drug-discovery | Drug discovery |
| awesome-molecular-generation | Molecular generation |
Biology & Proteins
| List | Focus |
|---|---|
| awesome-protein-design | Protein design papers |
| awesome-protein-design-software | Protein design tools |
| awesome-computational-biology | Computational biology |
Materials Science
| List | Focus |
|---|---|
| awesome-materials-informatics | Materials informatics |
| Best of Atomistic ML | Atomistic ML |
Methods & ML
| List | Focus |
|---|---|
| awesome-scientific-language-models | Scientific LLMs |
| awesome-scientific-machine-learning | SciML resources |
| awesome-pinn | Physics-informed NNs |