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Protein Sequences Python Packages

Python packages with the GitHub topic protein-sequences. Sorted by relevance, with stars and monthly downloads.
amckenna41
protpy

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

19K 17 1
williamgilpin
pypdb

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

5K 336 76
sacdallago
bio-embeddings

Get protein embeddings from protein sequences

3K 508 70
smaniches
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.

3K 2 0
lucidrains
protein-bert-pytorch

Implementation of ProteinBERT in Pytorch

3K 164 20
songlab-cal
tape-proteins

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

2K 739 135
AuReMe
esmecata

EsMeCaTa: Estimating Metabolic Capabilties from Taxonomy

2K 8 0
songlab-cal
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.

1K 739 135
HobnobMancer
cazy-webscraper

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

1K 18 2
bioinf-MCB
mdeepfri

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

1K 46 7
dohlee
abyssal-pytorch

Abyssal - Pytorch

836 6 2
dohlee
antiberty-pytorch

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

817 26 5
sacdallago
bio-embeddings-duongttr

Get protein embeddings from protein sequences

698 508 70
microsoft
evodiff

Generation of protein sequences and evolutionary alignments via discrete diffusion models

617 669 108
Sanpme66
protpeptigram

Visualization of Immunopeptides Mapped to Source Proteins Across Multiple Samples

557 0 0
dohlee
tranception-pytorch-dohlee

Tranception - Pytorch

518 3 0
univieCUBE
deepnog

Protein orthologous group assignment with deep learning

511 30 8
niklases
pypef

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

484 14 2
graph-part
graph-part

GraphPart, a data partitioning method for ML on biological sequences

442 35 6
kyegomez
progen-torch

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

333 11 0
joelb123
rafm

Reliable AlphaFold Measures

332 2 0
sbl-sdsc
mmtfpyspark

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

317 68 27
michaelscutari
protclust

Python tools for protein sequence clustering and dataset splitting

250 4 0
kklemon
protenc

Extract protein embeddings from protein language models.

238 10 1
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