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)

uniprot-mcp-server

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

bionemo-ir

Easy, fast, and memory-efficient structure prediction inference

cazy-webscraper

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

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.

mdeepfri

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

bio-embeddings

Get protein embeddings from protein sequences

pypef

PyPEF – Pythonic Protein Engineering Framework

evodiff

Generation of protein sequences and evolutionary alignments via discrete diffusion models

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.

graph-part

GraphPart, a data partitioning method for ML on biological sequences

protpeptigram

Visualization of Immunopeptides Mapped to Source Proteins Across Multiple Samples

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.

deepnog

Protein orthologous group assignment with deep learning

rafm

Reliable AlphaFold Measures

mmtfpyspark

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

protein-bert-pytorch

Implementation of ProteinBERT in Pytorch

protclust

protclust is a Python library for protein sequence analysis that integrates MMseqs2 for fast clustering and provides tools for creating robust machine learning datasets. It offers cluster-aware data splitting to prevent sequence similarity bias in model evaluation, along with comprehensive protein embedding capabilities for feature generation.

clean-fasta

A small, dependency-free command-line tool (and Python library) for cleaning and filtering FASTA sequence files. It strips gaps and whitespace, drops sequences that are too short, too long, malformed, or below a valid-character threshold, optionally removes duplicate identifiers, and writes tidy, line-wrapped FASTA output, along with a report.

folding

AlphaFold2 protein predictions

jamsfetch

Package for automatic data download from major bioinformatics databases

protenc

Extract protein embeddings the easy way.