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amckenna41
protpy

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

18K 17 1
williamgilpin
pypdb

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

5K 335 76
bioinf-MCB
mdeepfri

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

2K 45 7
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

From taxonomic affiliations to annotated consensus proteomes using UniProt database.

2K 8 0
sacdallago
bio-embeddings

Get protein embeddings from protein sequences

1K 508 70
HobnobMancer
cazy-webscraper

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

915 18 2
lucidrains
protein-bert-pytorch

Implementation of ProteinBERT in Pytorch

888 164 20
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.

806 739 135
niklases
pypef

PyPEF – Pythonic Protein Engineering Framework

685 14 2
dohlee
abyssal-pytorch

Abyssal - Pytorch

565 6 2
univieCUBE
deepnog

Protein orthologous group assignment with deep learning

527 30 8
graph-part
graph-part

Graph-based partitioning of biological sequence data

511 35 6
microsoft
evodiff

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

495 668 110
joelb123
rafm

Reliable AlphaFold Measures

477 2 0
Sanpme66
protpeptigram

Visualization of Immunopeptides Mapped to Source Proteins Across Multiple Samples

453 0 0
sbl-sdsc
mmtfpyspark

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

384 68 27
michaelscutari
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.

372 4 0
dohlee
tranception-pytorch-dohlee

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

343 3 0
kklemon
protenc

Extract protein embeddings the easy way.

342 10 1
dohlee
antiberty-pytorch

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

280 26 5
truemagic-coder
folding

AlphaFold2 protein predictions

212 0 0
kyegomez
progen-torch

Paper - Pytorch

202 11 0
sacdallago
bio-embeddings-duongttr

Get protein embeddings from protein sequences

200 508 70
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