Protein Sequences Python Packages

protpy

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

bio-embeddings

Get protein embeddings from protein sequences

pypdb

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

uniprot-mcp-server

Auditable UniProt MCP server with per-response SHA-256 provenance, release pinning, verification, and offline replay.

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.

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

From taxonomic affiliations to annotated consensus proteomes using UniProt database.

cazy-webscraper

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

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

mdeepfri

Pipeline for searching and aligning contact maps for proteins, then running DeepFri's GCN.

abyssal-pytorch

Implementation of Abyssal, a deep neural network trained with a new "mega" dataset to predict the impact of an amino acid variant on protein stability.

pypef

PyPEF – Pythonic Protein Engineering Framework

tranception-pytorch-dohlee

Implementation of Tranception, a SOTA transformer model for protein fitness prediction, in PyTorch.

deepnog

Protein orthologous group assignment with deep learning

protpeptigram

Mapping peptides to source protein for immunopeptidiomics data analysis

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"

protclust

Python tools for protein sequence clustering and dataset splitting

mmtfpyspark

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

rafm

Reliable AlphaFold Measures

jamsfetch

Package for automatic data download from major bioinformatics databases