Protein Sequences Python Packages

protpy

Python package for generating various biochemical, physicochemical and structural descriptors/features of protein sequences.

uniprot-mcp-server

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

pypdb

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

bionemo-ir

BioNeMo Inference Runtime: GPU accelerated framework for protein folding

cazy-webscraper

A tool to automate retrieving data from CAZy, build a local CAZyme SQL database, and throughly interrogating the data. Also, automate retrieving protein data, sequences, EC numbers and structure files for specific datasets in the CAZyme database from UniProt, GenBank and PDB.

tape-proteins

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

mdeepfri

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

esmecata

From taxonomic affiliations to annotated consensus proteomes using UniProt database.

bio-embeddings

A pipeline for protein embedding generation and visualization

pypef

A tool for performing data-driven protein engineering by building, testing, and inferring machine learning models trained on protein variant fitness data.

evodiff

Python package for generation of protein sequences and evolutionary alignments via discrete diffusion models

graph-part

Graph-based partitioning of biological sequence data

bio-embeddings-tape-proteins

Repostory of Protein Benchmarking and Modeling

protpeptigram

Mapping peptides to source protein for immunopeptidiomics data analysis

abyssal-pytorch

Abyssal - Pytorch

deepnog

Deep learning tool for protein orthologous group assignment

rafm

rafm

mmtfpyspark

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

protein-bert-pytorch

ProteinBERT - Pytorch

protclust

Python tools for protein sequence clustering and dataset splitting

clean-fasta

Clean and filter FASTA sequence files: strip gaps, filter by length and valid-character ratio, and deduplicate ids.

folding

ColabFold modified for AlphaFold2 and local installation

jamsfetch

JAMS-Fetch (Joint Automated Multi-source Sequence Fetcher) is a Python package. It automates the retrieval of sequence and structure data from major bioinformatics databases using a unified, user-friendly interface.

protenc

Extract protein embeddings from protein language models.