Protein Sequences Python Packages

protpy

Calculating a range of protein descriptors using their physicochemical, biological and structural properties 🔬.

pypdb

A Python API for the RCSB Protein Data Bank (PDB)

bio-embeddings

Get protein embeddings from protein sequences

uniprot-mcp-server

Model Context Protocol server for UniProt — Swiss-Prot and TrEMBL protein knowledgebase. 41 tools across 8 families with per-query SHA-256 provenance verification and offline replay.

protein-bert-pytorch

Implementation of ProteinBERT in Pytorch

tape-proteins

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.

esmecata

EsMeCaTa: Estimating Metabolic Capabilties from Taxonomy

bio-embeddings-tape-proteins

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.

cazy-webscraper

Web scraper to retrieve protein data catalogued by the CAZy, UniProt, NCBI, GTDB and PDB websites/databases.

mdeepfri

Pipeline for searching and aligning contact maps for proteins, and function prediction with DeepFRI.

abyssal-pytorch

Abyssal - Pytorch

antiberty-pytorch

An unofficial re-implementation of AntiBERTy, an antibody-specific protein language model, in PyTorch.

bio-embeddings-duongttr

Get protein embeddings from protein sequences

evodiff

Generation of protein sequences and evolutionary alignments via discrete diffusion models

protpeptigram

Visualization of Immunopeptides Mapped to Source Proteins Across Multiple Samples

tranception-pytorch-dohlee

Tranception - Pytorch

deepnog

Protein orthologous group assignment with deep learning

pypef

A tool for performing data-driven protein engineering by building machine learning models from protein variant fitness data.

graph-part

GraphPart, a data partitioning method for ML on biological sequences

progen-torch

Implementation of the model from "ProGen: Language Modeling for Protein Generation"

rafm

Reliable AlphaFold Measures

mmtfpyspark

Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.

protclust

Python tools for protein sequence clustering and dataset splitting

protenc

Extract protein embeddings from protein language models.