Top 30 protein open source projects

Official git repository for Biopython (originally converted from CVS)

✭ 2,936

python HTML c Parrot Roff Nu bioinformatics genomics dna protein-structure protein biopython phylogenetics sequence-alignment

r3dmol

🧬 An R package for visualizing molecular data in 3D

✭ 45

javascript r visualization protein-structure computational-biology molecular-graphics protein computational-chemistry htmlwidgets hacktoberfest 3d molecular-modeling

icn3d

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

✭ 95

javascript HTML nodejs webgl jupyter-notebook chemical protein snp nucleotide structure-viewer 3d-structure 3d-viewer molecular-viewer icn3d protein-viewer

FMol

A simplified drug discovery pipeline -- generating SMILE molecular with AlphaSMILES, predicting protein structure with AlphaFold, and checking the druggability with fpocket/Amber.

✭ 13

python matlab shell Makefile protein drug-discovery alphafold fpocket

EVcouplings

Evolutionary couplings from protein and RNA sequence alignments

✭ 113

Jupyter Notebook python protein structure-prediction 3d-structure protein-complexes

caviar

Protein cavity identification and automatic subpocket decomposition

✭ 27

python C++c pdb protein binding-pocket subpocket cavity-identification

cbh21-protein-solubility-challenge

Template with code & dataset for the "Structural basis for solubility in protein expression systems" challenge at the Copenhagen Bioinformatics Hackathon 2021.

✭ 15

python Dockerfile hackathon protein-structure protein drug-discovery solubility-prediction

orfipy

Fast and flexible ORF finder

✭ 27

python shell bioinformatics dna protein orf-detection orf-finder codon-tables extract-orfs orf-search

VSCoding-Sequence

VSCode Extension for interactively visualising protein structure data in the editor

✭ 41

typescript structural-biology pdb protein-structure structure vscode molecule protein vscode-extension pdb-files molstar

ProteinGCN

ProteinGCN: Protein model quality assessment using Graph Convolutional Networks

✭ 88

python shell deep-learning pytorch protein graph-convolutional-networks graph-neural-networks protein-model-quality-estimation

naf

Nucleotide Archival Format - Compressed file format for DNA/RNA/protein sequences

✭ 35

c perl Makefile compression dna file-format protein rna fasta fastq

cath-tools

Protein structure comparison tools such as SSAP and SNAP

✭ 40

C++HTML CMake bioinformatics biology pdb structure protein alignment ssap orengo cath superposition ucl cath-resolve-hits

SeqVec

Modelling the Language of Life - Deep Learning Protein Sequences

✭ 74

bioinformatics protein-structure protein protein-function

BuddySuite

Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files

✭ 106

python TeX workflow bioinformatics command-line biology dna protein phylogenetics alignment

FluentDNA

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.

✭ 52

javascript Jupyter Notebook python visualization bioinformatics sequencing liftover dna protein alignment fasta fluent ddv msa fasta-sequences bioinformatics-tool chain-alignment fluentdna

biovec

ProtVec can be used in protein interaction predictions, structure prediction, and protein data visualization.

✭ 23

python svm rbf-kernel word2vec protein gensim uniprot tsne biovec protein-vectors protein-visualization

lightdock

Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

gcWGAN

Guided Conditional Wasserstein GAN for De Novo Protein Design

✭ 38

Roff python protein-structure protein generative-model generative-adversarial-networks protein-design protein-sequence

deepblast

Neural Networks for Protein Sequence Alignment

✭ 29

python Jupyter Notebook protein-structure language-modeling protein neural-networks protein-sequences sequence-alignment structural-alignments

DeepAccNet

Pytorch/Python3 implementation of DeepAccNet, protein model accuracy evaluator.

✭ 57

python shell pytorch protein ema pyrosetta

FLIP

A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of protein design

✭ 35

Jupyter Notebook python protein protein-sequences representation-learning protein-design protein-function-prediction protein-fitness-prediction

pia

📚 🔬 PIA - Protein Inference Algorithms

✭ 19

java search-engine inference protein proteomics protein-inference spectrum-identification

EVE

Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning". Joint collaboration between the Marks lab and the OATML group.

✭ 37

python pytorch protein generative-model evolutionary-data eve-models

cgdms

Differentiable molecular simulation of proteins with a coarse-grained potential

✭ 44

python automatic-differentiation protein force-field potential coarse-grained

mmterm

View proteins and trajectories in the terminal

✭ 87

python visualization terminal protein-structure protein terminal-graphics trajectory

Jupyter Dock

Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.

✭ 179

Jupyter Notebook cheminformatics protein-structure jupyter-notebook computational-biology protein drug-discovery drug-repurposing rdkit openbabel drug-design mdanalysis autodock ledock molecular-docking autodock-vina py3dmol

pdb-tools

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

✭ 240

python TeX bioinformatics structural-biology pdb protein structural-bioinformatics utrecht-university rcsb

Deeprank-GNN

Graph Network for protein-protein interface

✭ 66

python graph protein

PBxplore

A suite of tools to explore protein structures with Protein Blocks 🐍

✭ 21

python structure protein bioinformatics-analysis

dnapacman

waka waka

✭ 15

python game dna pacman protein rna amino-acids

1-30 of 30 protein projects