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Protein Python Packages

Python packages with the GitHub topic protein. Sorted by relevance, with stars and monthly downloads.
biopython
biopython

Official git repository for Biopython (originally converted from CVS)

9M 5K 2K
mdshw5
pyfaidx

Efficient pythonic random access to fasta subsequences

480K 486 76
prody
prody

A Python Package for Protein Dynamics Analysis

55K 546 177
haddocking
pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.

33K 453 121
okkevaneck
prospr

Prospr is a universal toolbox for protein structure prediction within the HP-model. The Python package is based on a C++ core, which gives Prospr its high performance. The C++ core is made available as a separate zip file to facilitate high-performance computing applications. The package comes with many prediction algorithms and datasets to use.

9K 17 1
YaoYinYing
rosettapy

A Python utility for wrapping Rosetta command line tools.

8K 1 0
a-r-j
cpdb-protein

Cython implementation of PDB -> DataFrame parsing

6K 34 1
althonos
peptides

Physicochemical properties, indices and descriptors for amino-acid sequences.

6K 118 19
elkins
synth-pdb

Generate realistic PDB files with mixed secondary structures for testing, education and bioinformatics tool development

5K 1 0
a-r-j
graphein

Protein Graph Library

4K 1K 141
ncbi
icn3dpy

web-based protein structure viewer and analysis tool interactively or in batch mode

4K 174 53
urmi-21
orfipy

Fast and flexible ORF finder

3K 81 10
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
t03i
flatprot

A tool for 2D protein visualization aimed at improving the comparability of protein structures through standardized 2D visualizations.

2K 23 1
patrick-kidger
esm2quinox

An implementation of ESM2 in Equinox+JAX

2K 36 4
hgb-bin-proteomics
pyxlms

A python package to process protein cross-linking data.

2K 4 2
StollLab
chilife

Python package for site-directed spin labeling of proteins

2K 14 3
Jon-Ting
covdrugsim

Package to automate quantum mechanical calculations and molecular dynamics simulations of covalent drugs.

1K 1 0
murphycj
agfusion

Python package to annotate and visualize gene fusions.

1K 67 27
lignum-vitae
biobase

A comprehensive package of biological constants, serving as a foundational resource for biology and bioinformatics, complemented by functions to streamline related tasks.

1K 12 5
YaoYinYing
rosetta-finder

Searching for Rosetta Binaries.

1K 1 0
PixelgenTechnologies
pixelgen-pixelator

A command-line tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) and Proximity Network (PNA) assays.

1K 20 4
moshi4
cogclassifier

A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category

1K 83 6
biocentral
biocentral-api

Programmatic access to the biocentral ecosystem.

967 2 0
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