Ecosyste.ms: Packages

An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.

pypi.org "protein" keyword

usum 0.1.6
USUM: Plotting sequence similarity using USEARCH & UMAP
6 versions - Latest release: about 4 years ago - 1 dependent repositories - 87 downloads last month - 10 stars on GitHub - 2 maintainers
Top 1.9% on pypi.org
pyfaidx 0.8.1
pyfaidx: efficient pythonic random access to fasta subsequences
88 versions - Latest release: 4 months ago - 57 dependent packages - 268 dependent repositories - 111 thousand downloads last month - 440 stars on GitHub - 1 maintainer
peptides 0.3.2
Physicochemical properties, indices and descriptors for amino-acid sequences.
6 versions - Latest release: about 1 year ago - 1 dependent repositories - 454 downloads last month - 54 stars on GitHub - 2 maintainers
mini3di 0.1.0
A NumPy port of the foldseek code for encoding structures to 3di.
1 version - Latest release: about 18 hours ago - 12 stars on GitHub - 2 maintainers
caretta 0.1.2
Fast multiple protein structure alignment
3 versions - Latest release: over 2 years ago - 1 dependent repositories - 46 downloads last month - 24 stars on GitHub - 2 maintainers
mappings 0.1.0
Mapping and Analysis of Phosphorylation Pathways Identified through Network/Graph Signalling
4 versions - Latest release: over 2 years ago - 5 dependent repositories - 51 downloads last month - 1 stars on GitHub - 2 maintainers
batoms 2.4.0
A Python package for creating, editing and rendering atoms and molecules structures using Blender.
5 versions - Latest release: 6 months ago - 1 dependent repositories - 60 downloads last month - 123 stars on GitHub - 2 maintainers
rasp-pytorch 0.0.1
RaSP - Pytorch
1 version - Latest release: about 1 year ago - 21 downloads last month - 4 stars on GitHub - 2 maintainers
rich-msa 0.1.0
A Rich renderable for viewing Multiple Sequence Alignments in the terminal.
1 version - Latest release: almost 2 years ago - 1 dependent repositories - 33 downloads last month - 75 stars on GitHub - 2 maintainers
conphar 0.1.1
PyPharmer
2 versions - Latest release: 8 months ago - 24 downloads last month - 4 stars on GitHub - 2 maintainers
protkit 0.3.0
A unified toolkit for structural protein engineering.
8 versions - Latest release: 2 days ago - 189 downloads last month - 28 stars on GitHub - 2 maintainers
knot-pull 0.4.1
Simplifier of 3D structures of molecules
21 versions - Latest release: almost 5 years ago - 1 dependent repositories - 208 downloads last month - 8 stars on GitHub - 2 maintainers
Top 9.4% on pypi.org
molecularnodes 4.0.12
Toolbox for molecular animations with Blender and Geometry Nodes.
8 versions - Latest release: about 2 months ago - 1 dependent package - 1 dependent repositories - 191 downloads last month - 792 stars on GitHub - 2 maintainers
cogclassifier 1.0.5
A tool for classifying prokaryote protein sequences into COG functional category
7 versions - Latest release: over 1 year ago - 1 dependent repositories - 101 downloads last month - 37 stars on GitHub - 2 maintainers
proteinflow 2.8.0
Versatile pipeline for processing protein structure data for deep learning applications.
45 versions - Latest release: 3 months ago - 259 downloads last month - 165 stars on GitHub - 2 maintainers
configure-dms-viz 1.3.3
Configure your data for visualization with dms-viz.github.io
16 versions - Latest release: 16 days ago - 222 downloads last month - 0 stars on GitHub - 1 maintainer
Top 2.3% on pypi.org
prody 2.4.1
A Python Package for Protein Dynamics Analysis
65 versions - Latest release: 9 months ago - 6 dependent packages - 30 dependent repositories - 6.73 thousand downloads last month - 388 stars on GitHub - 1 maintainer
pyfamsa 0.4.0
Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence ali...
8 versions - Latest release: 5 days ago - 2.44 thousand downloads last month - 21 stars on GitHub - 2 maintainers
Top 0.6% on pypi.org
biopython 1.83
Freely available tools for computational molecular biology.
60 versions - Latest release: 4 months ago - 637 dependent packages - 3,405 dependent repositories - 832 thousand downloads last month - 3,908 stars on GitHub - 5 maintainers
mah51-biopython 1.1
Freely available tools for computational molecular biology.
2 versions - Latest release: about 2 years ago - 1 dependent repositories - 28 downloads last month - 3,900 stars on GitHub - 1 maintainer
covdrugsim 1.0.8
Package to automate quantum mechanical calculations and molecular dynamics simulations of covalen...
28 versions - Latest release: 4 days ago - 491 downloads last month - 1 stars on GitHub - 2 maintainers
alphaspace2 0.1.2
Protein topographical mapping tool
1 version - Latest release: over 3 years ago - 64 downloads last month - 21 stars on GitHub - 1 maintainer
protstruc 0.0.7
Utility library for handling protein structures in Python.
7 versions - Latest release: 9 months ago - 66 downloads last month - 2 stars on GitHub - 1 maintainer
sshmm 1.0.7
A sequence-structure hidden Markov model for the analysis of RNA-binding protein data.
11 versions - Latest release: almost 6 years ago - 1 dependent repositories - 59 downloads last month - 2 maintainers
protein-folding-gym-utils 0.0.1
Package with Reinforcement Learning Environments for Protein Folding
1 version - Latest release: 11 months ago - 18 downloads last month - 2 maintainers
pymut 0.1.1
Machine learning methods for the prediction of pathology in protein mutations, as in the PMut pre...
1 version - Latest release: about 7 years ago - 1 dependent repositories - 15 downloads last month - 6 stars on GitHub - 2 maintainers
proteingraph 0.3.0 💰
A package for making graph representations of proteinstructures.
6 versions - Latest release: over 3 years ago - 1 dependent repositories - 77 downloads last month - 57 stars on GitHub - 1 maintainer
isoformevent 0.0.1
Protein Isoform Event identifier
1 version - Latest release: over 1 year ago - 14 downloads last month - 2 maintainers
Top 4.0% on pypi.org
pdb-tools 2.5.0
A swiss army knife for PDB files.
38 versions - Latest release: almost 2 years ago - 2 dependent packages - 14 dependent repositories - 6.98 thousand downloads last month - 358 stars on GitHub - 1 maintainer
imaps 0.5.2
Bioinformatic pipelines for analysis of CLIP data
11 versions - Latest release: almost 4 years ago - 1 dependent repositories - 86 downloads last month - 0 stars on GitHub - 2 maintainers
cpdb-protein 0.2.0 💰
Cython implementation of PDB -> DataFrame parsing
3 versions - Latest release: 11 months ago - 50 downloads last month - 16 stars on GitHub - 2 maintainers
stringx 0.7.5
STRING DB API Client
11 versions - Latest release: about 1 month ago - 520 downloads last month - 1 stars on GitHub - 1 maintainer
deeprank-gnn 0.1.22
Graph Neural network Scoring of protein-protein conformations
4 versions - Latest release: almost 3 years ago - 1 dependent repositories - 58 downloads last month - 115 stars on GitHub - 4 maintainers
pyfferaph 0.0.1a4
PYthon Functions For Extended, Reproducible Analysis and graPH
9 versions - Latest release: over 3 years ago - 1 dependent repositories - 26 downloads last month - 1 maintainer
ginobifold 0.1.3
Simplified Af2 inference code
4 versions - Latest release: over 1 year ago - 14 downloads last month - 2 maintainers
Top 1.6% on pypi.org
py3dmol 2.1.0
An IPython interface for embedding 3Dmol.js views in Jupyter notebooks
29 versions - Latest release: about 2 months ago - 8 dependent packages - 30 dependent repositories - 115 thousand downloads last month - 757 stars on GitHub - 1 maintainer
psipredauto 0.0.1.1.1
Automated submission to the PSIPRED protein secondary structure calculator REST API.
2 versions - Latest release: about 2 years ago - 1 dependent repositories - 45 downloads last month - 1 stars on GitHub - 1 maintainer
bionorm 0.7.11
normalize, verify, and select genomic data
20 versions - Latest release: about 3 years ago - 108 downloads last month - 0 stars on GitHub - 4 maintainers
fastaframes 1.1.0
A very simple fasta file parser.
5 versions - Latest release: 7 months ago - 50 downloads last month - 2 stars on GitHub - 2 maintainers
sblu 0.7.2
Library for munging data files from ClusPro/FTMap/etc.
28 versions - Latest release: over 4 years ago - 2 dependent repositories - 340 downloads last month - 4 maintainers
lightdock 0.9.4 💰
A macromolecular docking framework
20 versions - Latest release: 9 months ago - 1 dependent repositories - 527 downloads last month - 259 stars on GitHub - 2 maintainers
isoelectric 1.0
IPC (Isoelectric Point Calculator) - prediction of isoelectric point of proteins and peptides
1 version - Latest release: over 4 years ago - 1 dependent repositories - 54 downloads last month - 2 maintainers
mercat2 1.4.1
versatile k-mer counter and diversity estimator for database independent property analysis (DIPA)...
8 versions - Latest release: 2 months ago - 1 dependent repositories - 37 downloads last month - 8 stars on GitHub - 4 maintainers
rosetta_dev_tools 1.1.0
A set of tools to facilitate development of the Rosetta protein design suite.
3 versions - Latest release: over 8 years ago - 2 dependent repositories - 13 downloads last month - 0 stars on GitHub - 2 maintainers
md-davis 0.4.1
A tool for comparative analysis of molecular dynamics simulations of proteins.
4 versions - Latest release: about 2 years ago - 1 dependent repositories - 121 downloads last month - 11 stars on GitHub - 2 maintainers
protgraph 0.3.10
ProtGraph, a graph generator for proteins.
19 versions - Latest release: 3 months ago - 1 dependent repositories - 138 downloads last month - 9 stars on GitHub - 1 maintainer
protflash 0.1.1
protein language model
2 versions - Latest release: 10 months ago - 66 downloads last month - 90 stars on GitHub - 2 maintainers
prospr 1.2.1
A toolbox for protein folding with Python.
59 versions - Latest release: 4 months ago - 1 dependent repositories - 1.5 thousand downloads last month - 18 stars on GitHub - 2 maintainers
proteinbert-pytorch-reproduction 0.0.2
ProteinBERT - Pytorch
1 version - Latest release: about 1 year ago - 22 downloads last month - 2 stars on GitHub - 2 maintainers
cluspro-api 1.1.0
Library for submitting and downloading job data from ClusPro.
5 versions - Latest release: about 5 years ago - 70 downloads last month - 2 maintainers
dispbind 1.0.2
Disorder protein genomic binding analysis toolkit
2 versions - Latest release: over 1 year ago - 15 downloads last month - 2 stars on GitHub - 1 maintainer
mdeepfri 1.1.5
Pipeline for searching and aligning contact maps for proteins, then running DeepFri's GCN.
5 versions - Latest release: about 1 month ago - 301 downloads last month - 27 stars on GitHub - 1 maintainer
kspider2 2.0.1
kSpider Python interface
2 versions - Latest release: almost 3 years ago - 1 dependent repositories - 45 downloads last month - 7 stars on GitHub - 2 maintainers
bpforms 0.0.16
Unambiguous representation of modified DNA, RNA, and proteins
12 versions - Latest release: almost 4 years ago - 7 dependent repositories - 116 downloads last month - 6 stars on GitHub - 4 maintainers
pdbx-mmcif 0.0.2
Parser for structures in the protein data bank (PDB) in the mmCIF format.
2 versions - Latest release: over 7 years ago - 1 dependent repositories - 11 downloads last month - 1 stars on GitHub - 2 maintainers
disembl 2.0rc0
A refactoring/reimplementation of DisEMBL
1 version - Latest release: over 7 years ago - 1 dependent repositories - 8 downloads last month - 0 stars on GitHub - 2 maintainers
berteome 0.1.6 💰
A library to analyze and explore protein sequences using BERT models
4 versions - Latest release: over 2 years ago - 1 dependent repositories - 50 downloads last month - 3 stars on GitHub - 2 maintainers
structuralia 0.912
A toolset to work with proteins
21 versions - Latest release: almost 6 years ago - 1 dependent repositories - 121 downloads last month - 0 stars on GitHub - 2 maintainers
hunana 1.0.7
HUNANA
8 versions - Latest release: about 3 years ago - 1 dependent repositories - 64 downloads last month - 6 stars on GitHub - 4 maintainers
protviewer 0.0.6
A web-based tool to visualize activities in proteins
6 versions - Latest release: almost 2 years ago - 1 dependent repositories - 23 downloads last month - 0 stars on GitHub - 2 maintainers
woolf 0.1.1
A tool to built machine learning classifiers for protein function differentiation
1 version - Latest release: almost 5 years ago - 1 dependent repositories - 10 downloads last month - 1 stars on GitHub - 2 maintainers
pifold-pytorch 0.0.1
Unofficial implementation of PiFold in PyTorch.
1 version - Latest release: 12 months ago - 13 downloads last month - 4 stars on GitHub - 2 maintainers
proteinworkshop 0.2.5 💰
Benchmarking framework for protein representation learning. Includes a large number of pre-traini...
10 versions - Latest release: 4 months ago - 1 dependent repositories - 83 downloads last month - 146 stars on GitHub - 2 maintainers
Top 8.8% on pypi.org
gauche 0.1.6
Gaussian Process Library for Molecules, Chemical Reactions and Proteins.
2 versions - Latest release: 5 months ago - 4 dependent repositories - 418 downloads last month - 174 stars on GitHub - 1 maintainer
pcmap 1.1.4
Computing contact map for protein structures
16 versions - Latest release: over 1 year ago - 1 dependent repositories - 202 downloads last month - 7 stars on GitHub - 1 maintainer
prodec 1.0.2
A package to calculate protein sequence descriptors
9 versions - Latest release: almost 2 years ago - 1 dependent package - 1 dependent repositories - 197 downloads last month - 1 stars on GitHub - 2 maintainers
progres 0.2.3
Fast protein structure searching using structure graph embeddings
8 versions - Latest release: 9 days ago - 237 downloads last month - 63 stars on GitHub - 1 maintainer
discere 0.0.4
Protein Feature Extraction package for Machine Learning
1 version - Latest release: over 4 years ago - 1 dependent repositories - 20 downloads last month - 16 stars on GitHub - 2 maintainers
alfpy 1.0.6
Alignment-free package to compare DNA/RNA/protein sequences (bioinformatics).
4 versions - Latest release: about 6 years ago - 1 dependent repositories - 93 downloads last month - 21 stars on GitHub - 1 maintainer
peatdb 2.3
Protein Engineering Analysis Tool
2 versions - Latest release: over 11 years ago - 1 dependent repositories - 30 downloads last month - 2 maintainers
Top 5.7% on pypi.org
graphein 1.7.6 💰
Protein & Interactomic Graph Construction for Machine Learning
30 versions - Latest release: 3 months ago - 1 dependent package - 3 dependent repositories - 1.5 thousand downloads last month - 927 stars on GitHub - 1 maintainer
kspider 2.3.2
A simple yet powerful sequence clustering tool
10 versions - Latest release: over 1 year ago - 1 dependent repositories - 210 downloads last month - 7 stars on GitHub - 1 maintainer
rnpfind 1.2.6
Collect and generate RNA-RBP interaction data in various formats
28 versions - Latest release: 4 months ago - 1 dependent repositories - 161 downloads last month - 6 stars on GitHub - 1 maintainer
dspp-keras 0.0.5
Integration of Database of structural propensities of proteins (dSPP) with Keras Machine Learning...
5 versions - Latest release: almost 7 years ago - 1 dependent repositories - 64 downloads last month - 166 stars on GitHub - 2 maintainers
dnacol 0.3.2
Display FASTA/FASTQ/SAM/VCF files with colored DNA/RNA bases and quality scores (`dnacol`) or a p...
3 versions - Latest release: almost 7 years ago - 1 dependent repositories - 12 downloads last month - 19 stars on GitHub - 2 maintainers
korbinian 0.3.4
Bioinformatic sequence analysis of membrane proteins.
2 versions - Latest release: almost 6 years ago - 1 dependent repositories - 22 downloads last month - 2 stars on GitHub - 2 maintainers
pyrotein 0.1.4
A tiny package for structure analysis of macromolecules.
5 versions - Latest release: about 3 years ago - 1 dependent repositories - 44 downloads last month - 3 stars on GitHub - 2 maintainers
motiffinder 0.0.2
A novel approach to motif identification in proteins
2 versions - Latest release: almost 5 years ago - 1 dependent repositories - 23 downloads last month - 1 stars on GitHub - 2 maintainers
openprotein 0.2.0
Open-Protein is an open source pre-training platform that supports multiple protein pre-training ...
2 versions - Latest release: about 1 year ago - 15 downloads last month - 2 maintainers
pairwise-sequence-alignment 1.0.0
Global and local pairwise alignments between nucleotide/protein sequences.
1 version - Latest release: about 1 year ago - 32 downloads last month - 4 stars on GitHub - 2 maintainers
rafm 1.1.4
rafm
10 versions - Latest release: over 2 years ago - 1 dependent repositories - 81 downloads last month - 1 stars on GitHub - 2 maintainers
310 0.1.0
A example Python package
1 version - Latest release: almost 2 years ago - 54 dependent repositories - 106 downloads last month - 21 stars on GitHub - 1 maintainer
alphabetsoup 0.5.3
tile phylogenetic space with subtrees
7 versions - Latest release: almost 4 years ago - 43 downloads last month - 0 stars on GitHub - 1 maintainer
prody-rhapsody 0.9.8
Python program, based on ProDy, for pathogenicity prediction of human missense variants.
6 versions - Latest release: about 4 years ago - 1 dependent repositories - 39 downloads last month - 7 stars on GitHub - 2 maintainers
protein 1.0.5
Quick UniProt protein search for the command line
9 versions - Latest release: about 4 years ago - 1 dependent repositories - 71 downloads last month - 1 stars on GitHub - 2 maintainers
arv 0.9.2
A fast 23andMe raw genome file parser
11 versions - Latest release: about 7 years ago - 221 downloads last month - 114 stars on GitHub - 1 maintainer
seqtables 0.11
Package for efficient analysis of next generation sequencing amplicon data using numpy and datafr...
2 versions - Latest release: over 4 years ago - 1 dependent repositories - 12 downloads last month - 5 stars on GitHub - 2 maintainers
pinfer 0.7.2
Inference of ancestral Protein Interaction Networks (PINs).
5 versions - Latest release: almost 8 years ago - 2 dependent repositories - 28 downloads last month - 0 stars on GitHub - 2 maintainers
seqvec 0.4.1
Embeeder tool for 'Modelling the Language of Life - Deep Learning Protein Sequences'
6 versions - Latest release: almost 4 years ago - 1 dependent package - 1 dependent repositories - 141 downloads last month - 109 stars on GitHub - 2 maintainers
azulejo 0.10.1
tile phylogenetic space with subtrees
26 versions - Latest release: over 3 years ago - 1 dependent repositories - 237 downloads last month - 0 stars on GitHub - 2 maintainers
complexconstructor 0.1.6
Generate macrocomplexes superimposing paired interacting elements.
4 versions - Latest release: about 4 years ago - 1 dependent repositories - 19 downloads last month - 0 stars on GitHub - 2 maintainers
abyssal-pytorch 0.0.5
Abyssal - Pytorch
4 versions - Latest release: about 1 year ago - 56 downloads last month - 6 stars on GitHub - 1 maintainer
orfipy 0.0.4
orfipy
4 versions - Latest release: almost 3 years ago - 1 dependent repositories - 261 downloads last month - 44 stars on GitHub - 2 maintainers
pull_into_place 1.2.2
A rosetta pipeline to position important protein sidechains with sub-angstrom accuracy.
8 versions - Latest release: about 7 years ago - 1 dependent repositories - 25 downloads last month - 5 stars on GitHub - 2 maintainers
thoipapy 1.2.0
Machine-learning prediction of residues driving homotypic transmembrane interactions.
12 versions - Latest release: over 3 years ago - 1 dependent repositories - 103 downloads last month - 2 stars on GitHub - 2 maintainers
bio-jade 1.0
A repository for modules and applications to aid in the design and analysis of Biological molecul...
1 version - Latest release: about 6 years ago - 1 dependent repositories - 23 downloads last month - 6 stars on GitHub - 2 maintainers
geomm 0.2.1
A simple no-nonsense library for computing common geometry on macromolecular systems.
11 versions - Latest release: about 1 year ago - 4 dependent repositories - 92 downloads last month - 4 stars on GitHub - 4 maintainers
buddysuite 1.4.0
BuddySuite is a collection of command line utilities written in Python for working with biologica...
14 versions - Latest release: over 2 years ago - 1 dependent repositories - 83 downloads last month - 121 stars on GitHub - 1 maintainer
foldingdiff-pytorch 0.0.3
Unofficial implementation of foldingdiff in PyTorch.
3 versions - Latest release: 12 months ago - 30 downloads last month - 7 stars on GitHub - 2 maintainers
Top 9.4% on pypi.org
protmapper 0.0.29
Map protein sites to human reference sequence.
27 versions - Latest release: 4 months ago - 1 dependent package - 8 dependent repositories - 2.41 thousand downloads last month - 4 stars on GitHub - 2 maintainers