AlphaFold Meets Flow Matching for Generating Protein Ensembles

EigenFold: Generative Protein Structure Prediction with Diffusion Models

A repository for modules and applications to aid in the design and analysis of Biological molecules. Replaced by Jade2

Pandas DataFrames for phylogenetics

Nature Biotechnology: Ultra-fast, sensitive detection of protein remote homologs using deep dense retrieval

Genome annotation with AUGUSTUS

Code for ColabDock paper

The official code for "TaxDiff: Taxonomic-Guided Diffusion Model for Protein Sequence Generation"

A Protein Large Language Model for Multi-Task Protein Language Processing

RADAR source code

Simple, lightweight package for genetic algorithms on molecules

Predict multiple protein conformations using sequence clustering and AlphaFold2.

A common units module for the OpenFF software stack

The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at https://open-forcefield-toolkit.readthedocs.io

CHARMM and AMBER forcefields for OpenMM (with small molecule support)

A tool to convert IUPAC representations of glycans into SMILES strings.

NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model

repo for DynamicBind: Predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model

NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood https://www.iqtree.org

⚡ ♒ Rapid prokaryotic genome annotation

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

CNV Rapid Aberration Detection And Reporting

Python code to color a PDB structure based on parameters from a multiple sequence alignment

The Nutmeg machine learning models

OpenMM plugin to define forces with neural networks

Implementation of Alphafold 3 in Pytorch