Snakemake pipeline for Rosetta 'cartesian-ddg' protocol for protein stability prediction upon mutations.

Fast deep learning methods for large-scale protein-protein interaction screening

Bare-bones implementations of some generative models in Jax: diffusion, normalizing flows, consistency models, flow matching, (beta)-VAEs, etc

Novel estimator for the change in stability upon point mutation in monomeric and multimeric proteins.

Weave is a toolkit for developing AI-powered applications, built by Weights & Biases.

Parse PDB to UniProt data from SIFTS (pdb_chain_uniprot.tsv) to map ELM entries to PDB ss and disorder information.

Python package for handling ModelCIF mmCIF and BinaryCIF files

CArbohydrate-Protein Site IdentiFier

This is the public repository for the RING PyMOL plugin developed by the BioComputing UP laboratory at the University of Padua

A simplified implementation of DSSP algorithm for PyTorch and NumPy

Printing text using protein structures

Friends don't let friends make certain types of data visualization - What are they and why are they bad.

Predict disorder and disorder binding from AlphaFold structures

EquiDock: geometric deep learning for fast rigid 3D protein-protein docking

A comprehensive library for computational molecular biology

Foldseek enables fast and sensitive comparisons of large structure sets.

Open source code for AlphaFold to extract protein embeddings

A library of free open source icons for science illustrations in biology and chemistry

a JavaScript DNA, RNA, and protein sequence viewer

Uncovering phosphorylation–based specificities through functional interaction networks

Pipeline to extract protein interfaces from Interactome3d structures

Estimate PTM hotspots in protein sequence alignments

Genomic Interactive Visualization Engine

caret (Classification And Regression Training) R package that contains misc functions for training and plotting classification and regression models