Protein Structure

Structure prediction tools, multimer prediction, and structural databases.

Tools Datasets Getting Started

Tools

Structure Prediction

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

Multimer & Complex Prediction

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

Visualization & Analysis

PyMOL Molecular visualization ChimeraX Molecular visualization for structural biology BioPython Python tools for biological computation ProDy Protein dynamics analysis

Datasets

Structures

PDB Experimental structures 200K+ AlphaFold DB Predicted protein structures 200M+ structures

Sequences

UniProt Protein sequences & functions 250M+ Uniclust Clustered protein sequences

Classification & Annotation

CATH Protein domain classification Human Protein Atlas Protein expression data

Getting Started


conda create -n proteins python=3.10
conda activate proteins
 
pip install biopython fair-esm

Protein Design Single-Cell & Genomics