Biology Tools

Software libraries for drug discovery and computational biology.

Deep Learning for Life Sciences

Tool	Description	Link
DeepChem	Comprehensive ML library for drug discovery	deepchem.io
DGL-LifeSci	GNN library for life science applications	github
Chemprop	Message passing neural networks	github
TorchDrug	GNN-based drug discovery library	torchdrug.ai
DeepPurpose	Deep learning for drug-target interaction	github

Protein Structure Prediction

Tool	Description	Link
AlphaFold3	Advanced modeling with ligands, nucleotides, PTMs	github
AlphaFold2	Protein structure prediction	alphafold.ebi.ac.uk
ESM/ESMFold	Protein language models & fast structure prediction	github
ColabFold	Community notebooks for AF2, ESMFold, RoseTTAFold	github
OpenFold	PyTorch reimplementation of AlphaFold2	github
RoseTTAFold	Three-track neural network for structure	github
OmegaFold	Single-sequence structure prediction	github
Boltz-1	Unified prediction for proteins, RNA, DNA, ligands	github
Chai-1	Proteins, small molecules, DNA, RNA with restraints	github

Protein Design

Tool	Description	Link
ProteinMPNN	Message passing for inverse folding	github
RFDiffusion	Diffusion model for backbone generation	github
ColabDesign	Notebooks for AfDesign, TrDesign, ProteinMPNN	github
ESM-IF1	Inverse folding with ESM	github
EvoDiff	Discrete diffusion for sequences	github
ProtGPT2	GPT-2 based sequence generation	huggingface
BindCraft	Binder design	github
LM-Design / ByProt	Language model design	github
ProteinSolver	Graph neural network for constraint-based design	github
ECNet	Fine-tunable fitness/function prediction	github

Protein Language Models

Model	Description	Link
ESM-2	Protein embeddings (8M-15B params)	github
ProtTrans	Transformer embeddings for proteins	github
AMPLIFY	ESM2 reimplementation with open training	github
PoET	Variant effect prediction and generation	github
EvoProtGrad	MCMC-based directed evolution	github

Multimer & Complex Prediction

Tool	Description	Link
AlphaFold2-Multimer	Protein complex prediction	github
AlphaPulldown	Protein-protein interaction screening	github
AF2Complex	Complex assembly	github
PeSTo	Interface residue prediction	github

Visualization & Analysis

Tool	Description	Link
PyMOL	Molecular visualization	pymol.org
ChimeraX	Molecular visualization for structural biology	rbvi.ucsf.edu
BioPython	Python tools for biological computation	biopython.org
ProDy	Protein dynamics analysis	prody.csb.pitt.edu

Single-Cell Analysis

Tool	Description	Link
Scanpy	Single-cell analysis in Python	scanpy.readthedocs.io
Seurat	Single-cell analysis in R	satijalab.org/seurat
Squidpy	Spatial transcriptomics analysis	squidpy.readthedocs.io
scGPT	Transformer model for single-cell	github
scFoundation	Single-cell foundation model	github
scPRINT	Cell imputation model	github
Open Problems	Community benchmarking platform for single-cell methods — tasks, metrics, and leaderboards	openproblems.bio

Drug Discovery Platforms

Tool	Description	Link
RDKit	Core cheminformatics toolkit	rdkit.org
Open Drug Discovery Toolkit	ADMET prediction	github
TDC	Therapeutics Data Commons	tdcommons.ai

Drug-Target Interaction

Tool	Description	Link
NeoDTI	Drug-target interaction prediction	github
TransformerCPI	Transformer for compound-protein interaction	github
drGAT	Attention-based drug response predictor	github

Biological Language Models

Model	Description	Link
ESM-2	Protein embedding models	github
ChemBERTa-2	Chemical SMILES embeddings	github
BioGPT	Biomedical text generation	github
GeneGPT	Biomedical information system	github
GenePT	Single-cell foundation model	github

Network & Pathway Analysis

Tool	Description	Link
STRING	Protein-protein interaction networks	string-db.org
Cytoscape	Network visualization and analysis	cytoscape.org
PathwayCommons	Biological pathway data	pathwaycommons.org

Awesome Lists

List	Focus
awesome-protein-design	Protein design papers
awesome-protein-design-software	Protein design tools
awesome-AI-based-protein-design	AI protein design
awesome-computational-biology	Computational biology resources
awesome-small-molecule-ml	Drug discovery ML
awesome-drug-discovery	Drug discovery tools

Getting Started


conda create -n bio python=3.10
conda activate bio
 
# Core tools
pip install deepchem rdkit
 
# For protein work
pip install biopython fair-esm
 
# For single-cell
pip install scanpy squidpy