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protein
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146 search results found
Biopython
⭐
3,918
Official git repository for Biopython (originally converted from CVS)
Awesome Deepbio
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1,467
A curated list of awesome deep learning applications in the field of computational biology
Graphein
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932
Protein Graph Library
Deeppurpose
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826
A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)
Biotite
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515
A comprehensive library for computational molecular biology
Hh Suite
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429
Remote protein homology detection suite.
Pyfaidx
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427
Efficient pythonic random access to fasta subsequences
Bakta
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365
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
Plip
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320
Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294
Pdb Tools
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319
A dependency-free cross-platform swiss army knife for PDB files.
Pygeno
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242
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
Kaiju
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236
Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
Lightdock
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234
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
Hgvs
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226
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
Pronto
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212
A Python frontend to (Open Biomedical) Ontologies.
P2rank
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193
P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.
Imgthla
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178
Github for files currently published in the IPD-IMGT/HLA FTP Directory hosted at the European Bioinformatics Institute
Metaeuk
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142
MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics
Bio4j
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112
Bio4j abstract model and general entry point to the project
Biojava Tutorial
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111
📖📚An introductory tutorial for BioJava
Run_dbcan
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109
Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.
Buddysuite
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105
Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files
Philosopher
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104
A complete toolkit for shotgun proteomics data analysis
Deeplearning In Bioinformatics
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104
For anyone who are eager to applying deep learning in bioinformatics!
Nightingale
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102
Data visualisation web components for the life sciences.
Seqvec
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101
Modelling the Language of Life - Deep Learning Protein Sequences
Famsa
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101
Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)
Plass
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99
Protein-Level ASSembler (PLASS): sensitive and precise protein assembler
Biostructures.jl
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77
A Julia package to read, write and manipulate macromolecular structures (particularly proteins)
Prodigy
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76
Predict the binding affinity of protein-protein complexes from structural data
Haddock3
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76
Official repo of the modular BioExcel version of HADDOCK
Peptides
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71
An R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences.
Pyfeat
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68
A Python-based Effective Feature Generation Tool from DNA, RNA, and Protein Sequences
Mitos.jl
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64
Mutual Information Tools for protein Sequence analysis in Julia
Pymod
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61
PyMod 3 - sequence similarity searches, multiple sequence/structure alignments, and homology modeling within PyMOL.
Awesome Structural Bioinformatics
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54
Structural Bioinformatics is awesome. Throw your textbook in the garbage, light the garbage can on fire, and blend the ashes into your cold brew almond milk latte and read this.
Neodti
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54
NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions
Genotify
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51
A minimal desktop app for easy and convenient gene annotation.
Bio
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51
Bioinformatics utilities.
Cath Tools
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51
Protein structure comparison tools such as SSAP and SNAP
Paladin
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50
Protein Alignment and Detection Interface
Protr
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50
🧬 Toolkit for generating various numerical features of protein sequences
Mantis
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50
A package to annotate protein sequences
Bioblender21
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47
Blender plugin to process biological data and molecular work.
Agfusion
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46
Python package to annotate and visualize gene fusions.
Cell2cell
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44
User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
Fluentdna
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43
FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.
Peptide Shaker
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41
Interpretation of proteomics identification results
Pfeature
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41
A software package for computing features of peptides and proteins
Megadock
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38
An ultra-high-performance protein-protein docking for heterogeneous supercomputers
Peptides.py
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36
Physicochemical properties, indices and descriptors for amino-acid sequences.
Dips Plus
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34
The Enhanced Database of Interacting Protein Structures for Interface Prediction
Deepinteract
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33
A geometric deep learning pipeline for predicting protein interface contacts.
Protwis
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31
Protwis is the backbone of the GPCRdb. The GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs).
Nolabs
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30
Open source biolab
Biomedical Nlp Corpus
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29
Corpus (datasets) collection about biology and medical NLP.
Rcpi
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28
Molecular informatics toolkit with a comprehensive integration of bioinformatics and cheminformatics tools for drug discovery.
Phylostratr
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28
An R framework for phylostratigraphy
Cogclassifier
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27
A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category
Pdb Benchmarks
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26
Benchmarking common tasks on proteins in various languages and packages
Orfipy
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25
Fast and flexible ORF finder
Kinfin
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24
Taxon-aware analysis of clustered protein sequences
Electrostatics.github.io
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23
APBS & PDB2PQR - software for biomolecular electrostatics and solvation
Sequencework
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22
programs and scripts, mainly python, for analyses related to nucleic or protein sequences
Lexicon
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22
Data visualization library for creating interactive graphs and dashboards for bioinformatics etc.
Rosalind Solutions
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21
my solutions to problems from Rosalind.
Lightdock Python2.7
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20
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
Reactomepy
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19
Explore biomolecular pathways in Reactome from the command-line or a Python script
Gaussdca.jl
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18
Multivariate Gaussian Direct Coupling Analysis for residue contact prediction in protein families - Julia module
Netsmooth
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18
netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation
Correlationplus
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18
A Python package to calculate, visualize and analyze correlation maps of proteins.
Prospr
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17
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.
Genome_collector
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17
🌠 Easily download genomes and build BLAST/Bowtie indexes in Python
Plink2
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17
pLink is a software dedicated for the analysis of chemically cross-linked proteins or protein complexes using mass spectrometry.
Deepcoil
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16
Fast and accurate prediction of coiled coil domains in protein sequences.
Amoebae
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14
Workflow for identifying and classifying homologous gene/protein sequences
Bindpredict
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14
Prediction of binding residues for metal ions, nucleic acids, and small molecules.
Bmi219 2017 Proteinfolding
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14
UCSF BMI219 Deep Learning (2017), Coding example (Prediction of protein folding with RNN and CNN)
Bioinformatics
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14
Bioinformatics Workflows
Hypothesis Bio
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14
Hypothesis extension for computational biology
Biocor
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14
Package to calculate functional similarity between genes https://biocor.llrs.dev
De Stress
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13
DE-STRESS is a model evaluation pipeline that aims to make protein design more reliable and accessible.
Lightdock Rust
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13
A Rust implementation of the LightDock macromolecular docking software
Lib310
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13
lib310 python package
Emg Toolkit
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13
MGnify API toolkit
Respre
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13
ResPRE is an algorithm for protein residue-residue contact-map prediction
Biobtree
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13
A bioinformatics tool to search, map and retrieve identifiers, keywords and attributes
Proteinsolver
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12
Graph neural network capable of generating novel amino acid sequences that fold into proteins with predetermined topologies.
Pfind3
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12
Proteindf
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12
Canonical (Kohn-Sham) molecular orbital calculation software for large molecules such as protein
Phagehosts
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11
This is the complete code base used in Robert A. Edwards, Katelyn McNair, Karoline Faust, Jeroen Raes, and Bas E. Dutilh (2015) Computational approaches to predict bacteriophage–host relationships. FEMS Microbiology Reviews doi: 10.1093/femsre/fuv048
Mmtf Proteomics
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11
Methods for mapping proteomics data on 3D protein structure.
Neurobind
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11
Yet Another Model Using Neural Networks for Predicting Binding Preferences of for Test DNA Sequences
Gotranseq
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11
convert nucleic sequence in protein sequence
Photon
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11
PHOsphoproteomic dissecTiOn using Networks
Pose
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10
A bare metal Python library for building and manipulating protein molecular structures
Programming For Bioinformatics
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10
Protein Feature Extraction
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10
Python code to extract features from Protein sequences for Machine Learning/Deep Learning
Cazy_webscraper
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10
Web scraper to retrieve protein data catalogued by the CAZy, UniProt, NCBI, GTDB and PDB websites/databases.
Sequence Database Curator
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10
This program dereplicates and/or filter nucleotide and/or protein database from a list of names or sequences (by exact match).
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