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)

mdeepfri

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

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.

bio-embeddings

Get protein embeddings from protein sequences

protein-bert-pytorch

Implementation of ProteinBERT in Pytorch

cazy-webscraper

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

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.

pypef

PyPEF – Pythonic Protein Engineering Framework

abyssal-pytorch

Abyssal - Pytorch

deepnog

Protein orthologous group assignment with deep learning

graph-part

Graph-based partitioning of biological sequence data

evodiff

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

protpeptigram

Visualization of Immunopeptides Mapped to Source Proteins Across Multiple Samples

rafm

Reliable AlphaFold Measures

tranception-pytorch-dohlee

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

mmtfpyspark

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

protenc

Extract protein embeddings the easy way.

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

progen-torch

Paper - Pytorch

jamsfetch

Package for automatic data download from major bioinformatics databases