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Stars
Official repository for the Boltz-1 biomolecular interaction model
Inference code for scalable emulation of protein equilibrium ensembles with generative deep learning
Sidechain conditioning and modeling for full-atom protein sequence design
Python packaging and dependency management made easy
A tool for generating .pex (Python EXecutable) files, lock files and venvs.
A modern Python package and dependency manager supporting the latest PEP standards
PyPI generator, backed entirely by static files
PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
We introduce a differentiable approach to phylogenetic tree construction, optimizing tree and ancestral sequences in its original representation itself, thus requiring no prior training data.
Model for predicting micro-millisecond motions from protein sequence and/or structure
Analysis of non-covalent interactions in MD trajectories
All-atom protein generation using latent diffusion, with compositional function and taxonomic prompts. http://bit.ly/plaid-proteins
Chai-1, SOTA model for biomolecular structure prediction
Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model
Public RFDiffusionAA repo
Optimizing AlphaFold Training and Inference on GPU Clusters
A trainable PyTorch reproduction of AlphaFold 3.
MaSIF-neosurf: surface-based protein design for ternary complexes.
MaSIF- Molecular surface interaction fingerprints. Geometric deep learning to decipher patterns in molecular surfaces.
An open-source Python package for the visual annotation of proteomics data with sequence specific knowledge.
A flexible package manager that supports multiple versions, configurations, platforms, and compilers.
Visualization for peptides and their bioactive functions