Ecosyste.ms: Repos

An open API service providing repository metadata for many open source software ecosystems.

GitHub topics: protein

Repositories

biopython/biopython

Official git repository for Biopython (originally converted from CVS)

Language: Python - Size: 67.9 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 4,182 - Forks: 1,720

a-r-j/graphein

Protein Graph Library

Language: Jupyter Notebook - Size: 87.8 MB - Last synced: 2 days ago - Pushed: 12 days ago - Stars: 987 - Forks: 122

BradyAJohnston/MolecularNodes

Toolbox for molecular animations in Blender, powered by Geometry Nodes.

Language: Python - Size: 742 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 796 - Forks: 81

salesforce/progen

Official release of the ProGen models

Language: Python - Size: 62.5 KB - Last synced: about 1 month ago - Pushed: 10 months ago - Stars: 555 - Forks: 107

flowhub-team/awesome-omics

A collection of awesome things regarding all omics.

Size: 123 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 535 - Forks: 61

microsoft/foldingdiff

Diffusion models of protein structure; trigonometry and attention are all you need!

Language: Jupyter Notebook - Size: 228 MB - Last synced: 5 days ago - Pushed: 5 months ago - Stars: 462 - Forks: 47

mdshw5/pyfaidx

Efficient pythonic random access to fasta subsequences

Language: Python - Size: 11.7 MB - Last synced: 5 days ago - Pushed: 20 days ago - Stars: 441 - Forks: 73

prody/ProDy

A Python Package for Protein Dynamics Analysis

Language: Python - Size: 127 MB - Last synced: 1 day ago - Pushed: 8 days ago - Stars: 390 - Forks: 140

haddocking/pdb-tools

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

Language: Python - Size: 950 KB - Last synced: 9 days ago - Pushed: 17 days ago - Stars: 358 - Forks: 111

lightdock/lightdock

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

Language: Python - Size: 93 MB - Last synced: 11 days ago - Pushed: 4 months ago - Stars: 276 - Forks: 35

fogleman/ribbon

Ribbon diagrams of proteins in #golang.

Language: Go - Size: 778 KB - Last synced: 29 days ago - Pushed: about 2 years ago - Stars: 242 - Forks: 24

AngelRuizMoreno/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.

Language: Jupyter Notebook - Size: 30.8 MB - Last synced: about 2 months ago - Pushed: 7 months ago - Stars: 240 - Forks: 58

westlake-repl/SaProt

Saprot: Protein Language Model with Structural Alphabet

Language: Python - Size: 1.99 MB - Last synced: about 13 hours ago - Pushed: 1 day ago - Stars: 220 - Forks: 19

Lattice-Automation/seqviz

a JavaScript DNA, RNA, and protein sequence viewer

Language: TypeScript - Size: 112 MB - Last synced: 10 days ago - Pushed: about 1 month ago - Stars: 213 - Forks: 48

debbiemarkslab/EVcouplings

Evolutionary couplings from protein and RNA sequence alignments

Language: Jupyter Notebook - Size: 18.3 MB - Last synced: 21 days ago - Pushed: 4 months ago - Stars: 212 - Forks: 70

zjunlp/Mol-Instructions

[ICLR 2024] Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language Models

Language: Python - Size: 16.6 MB - Last synced: 10 days ago - Pushed: 11 days ago - Stars: 186 - Forks: 12

opendilab/awesome-AI-based-protein-design

A collection of research papers for AI-based protein design

Size: 543 KB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 186 - Forks: 12

PeptoneLtd/dspp-keras

Protein order and disorder data for Keras, Tensor Flow and Edward frameworks with automated update cycle made for continuous learning applications.

Language: Python - Size: 74.2 KB - Last synced: 2 days ago - Pushed: almost 2 years ago - Stars: 166 - Forks: 21

a-r-j/ProteinWorkshop

Benchmarking framework for protein representation learning. Includes a large number of pre-training and downstream task datasets, models and training/task utilities. (ICLR 2024)

Language: Python - Size: 21.4 MB - Last synced: about 10 hours ago - Pushed: 26 days ago - Stars: 153 - Forks: 13

ncbi/icn3d

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

Language: JavaScript - Size: 390 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 144 - Forks: 42

Shen-Lab/DeepAffinity

Protein-compound affinity prediction through unified RNN-CNN

Language: Python - Size: 307 MB - Last synced: 10 days ago - Pushed: over 1 year ago - Stars: 133 - Forks: 30

HICAI-ZJU/Scientific-LLM-Survey

Scientific Large Language Models: A Survey on Biological & Chemical Domains

Size: 591 KB - Last synced: 21 days ago - Pushed: 21 days ago - Stars: 128 - Forks: 10

beautiful-atoms/beautiful-atoms

Python module for drawing and rendering beautiful atoms and molecules using Blender.

Language: Python - Size: 12.8 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 123 - Forks: 21

biologyguy/BuddySuite

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

Language: Python - Size: 269 MB - Last synced: 17 days ago - Pushed: over 2 years ago - Stars: 121 - Forks: 23

bio4j/bio4j

Bio4j abstract model and general entry point to the project

Language: Java - Size: 273 MB - Last synced: about 2 months ago - Pushed: over 7 years ago - Stars: 119 - Forks: 19

DeepRank/Deeprank-GNN 📦

Graph Network for protein-protein interface

Language: Python - Size: 96 MB - Last synced: 10 days ago - Pushed: about 2 months ago - Stars: 115 - Forks: 29

Rostlab/SeqVec Fork of mheinzinger/SeqVec

Modelling the Language of Life - Deep Learning Protein Sequences

Language: Python - Size: 11.7 MB - Last synced: 16 days ago - Pushed: over 3 years ago - Stars: 110 - Forks: 14

malllabiisc/ProteinGCN

ProteinGCN: Protein model quality assessment using Graph Convolutional Networks

Language: Python - Size: 4.99 MB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 109 - Forks: 19

chao1224/ChatDrug

LLM for Drug Editing, ICLR 2024

Language: Python - Size: 4.48 MB - Last synced: 3 months ago - Pushed: 4 months ago - Stars: 108 - Forks: 8

jgreener64/mmterm

View proteins and trajectories in the terminal

Language: Python - Size: 570 KB - Last synced: 4 months ago - Pushed: almost 4 years ago - Stars: 102 - Forks: 8

flatironinstitute/deepblast

Neural Networks for Protein Sequence Alignment

Language: Python - Size: 56.7 MB - Last synced: 23 days ago - Pushed: about 1 month ago - Stars: 96 - Forks: 16

molstar/VSCoding-Sequence

VSCode Extension for interactively visualising protein structure data in the editor

Language: TypeScript - Size: 89.3 MB - Last synced: 14 days ago - Pushed: over 1 year ago - Stars: 92 - Forks: 8

zjunlp/OntoProtein

Code and datasets for the ICLR2022 paper "OntoProtein: Protein Pretraining With Gene Ontology Embedding"

Language: Python - Size: 649 KB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 92 - Forks: 19

swsoyee/r3dmol

🧬 An R package for visualizing molecular data in 3D

Language: JavaScript - Size: 31.4 MB - Last synced: 1 day ago - Pushed: 7 months ago - Stars: 88 - Forks: 4

J-SNACKKB/FLIP

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

Language: Jupyter Notebook - Size: 595 MB - Last synced: 2 days ago - Pushed: 11 months ago - Stars: 84 - Forks: 12

j3xugit/RaptorX-Contact

Deep residual neural network for protein contact/distance prediction developed by Xu group

Language: Python - Size: 183 KB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 72 - Forks: 22

hiranumn/DeepAccNet

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

Language: Python - Size: 837 MB - Last synced: 3 months ago - Pushed: almost 3 years ago - Stars: 72 - Forks: 11

royerlab/cytoself

Self-supervised models for encoding protein localization patterns from microscopy images

Language: Python - Size: 50.2 MB - Last synced: 24 days ago - Pushed: 6 months ago - Stars: 69 - Forks: 13

food-nutrients/food-nutrients

:fork_and_knife: Food Nutrients

Language: JavaScript - Size: 3.12 MB - Last synced: 3 months ago - Pushed: over 1 year ago - Stars: 68 - Forks: 25

pub-calculator-io/protein-calculator

Free WordPress Plugin: Relying on certain statistics and recommendations, this free protein calculator predicts how much protein a person needs each day to be healthy. www.calculator.io/protein-calculator/

Language: JavaScript - Size: 6.46 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 65 - Forks: 0

josiahseaman/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.

Language: JavaScript - Size: 71.1 MB - Last synced: 3 months ago - Pushed: almost 3 years ago - Stars: 60 - Forks: 7

tadorfer/protlearn

A Python package for extracting protein sequence features

Language: Python - Size: 9.84 MB - Last synced: 17 days ago - Pushed: over 1 year ago - Stars: 58 - Forks: 8

twoXes/awesome-structural-bioinformatics

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.

Language: Python - Size: 31.1 MB - Last synced: about 14 hours ago - Pushed: about 1 year ago - Stars: 56 - Forks: 9

jpquast/protti

Picotti lab data analysis package.

Language: R - Size: 37.6 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 56 - Forks: 5

songlab-cal/factored-attention

This repository contains code for reproducing results in our paper Interpreting Potts and Transformer Protein Models Through the Lens of Simplified Attention

Language: Jupyter Notebook - Size: 27.4 MB - Last synced: 28 days ago - Pushed: over 1 year ago - Stars: 55 - Forks: 9

althonos/peptides.py

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

Language: Python - Size: 175 KB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 54 - Forks: 9

murphycj/AGFusion

Python package to annotate and visualize gene fusions.

Language: Python - Size: 345 MB - Last synced: 23 days ago - Pushed: about 2 months ago - Stars: 54 - Forks: 25

UCLOrengoGroup/cath-tools

Protein structure comparison tools such as SSAP and SNAP

Language: C++ - Size: 18.8 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 51 - Forks: 14

psipred/cgdms

Differentiable molecular simulation of proteins with a coarse-grained potential

Language: Python - Size: 47.9 MB - Last synced: 30 days ago - Pushed: about 2 years ago - Stars: 51 - Forks: 4

ostrokach/proteinsolver

Graph neural network for generating novel amino acid sequences that fold into proteins with predetermined topologies.

Language: Jupyter Notebook - Size: 271 MB - Last synced: 2 months ago - Pushed: about 3 years ago - Stars: 49 - Forks: 8

urmi-21/orfipy

Fast and flexible ORF finder

Language: Python - Size: 5.3 MB - Last synced: 12 days ago - Pushed: over 2 years ago - Stars: 47 - Forks: 6

KirillKryukov/naf

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

Language: C - Size: 708 KB - Last synced: 7 months ago - Pushed: about 2 years ago - Stars: 47 - Forks: 6

OATML/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.

Language: Python - Size: 8.61 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 44 - Forks: 47

wells-wood-research/timed-design

Protein Sequence Design with Deep Learning and Tooling like Monte Carlo Sampling and Analysis

Language: Python - Size: 31.4 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 42 - Forks: 10

moshi4/COGclassifier

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

Language: Python - Size: 29.5 MB - Last synced: 6 days ago - Pushed: 6 months ago - Stars: 39 - Forks: 5

jr-marchand/caviar

// PROJECT PAUSED FOR NOW (lack of capacity) // Protein cavity identification and automatic subpocket decomposition

Language: Python - Size: 26 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 36 - Forks: 10

Shen-Lab/gcWGAN

Guided Conditional Wasserstein GAN for De Novo Protein Design

Language: Roff - Size: 334 MB - Last synced: 10 days ago - Pushed: about 3 years ago - Stars: 36 - Forks: 7

clemgoub/TE-Aid

Annotation helper tool for the manual curation of transposable element consensus sequences

Language: R - Size: 2.13 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 35 - Forks: 6

QizhiPei/SSM-DTA

SSM-DTA: Breaking the Barriers of Data Scarcity in Drug-Target Affinity Prediction (Briefings in Bioinformatics 2023)

Language: Python - Size: 1.12 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 34 - Forks: 4

zjunlp/NLP4SciencePapers

Must-read papers on NLP for science.

Size: 74.2 KB - Last synced: 9 months ago - Pushed: 11 months ago - Stars: 34 - Forks: 3

DeepGraphLearning/SiamDiff

Code for Pre-training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction (https://arxiv.org/abs/2301.12068)

Language: Python - Size: 1.86 MB - Last synced: 10 days ago - Pushed: 10 months ago - Stars: 32 - Forks: 4

drostlab/metablastr

Seamless Integration of BLAST Sequence Searches in R

Language: R - Size: 656 KB - Last synced: about 2 months ago - Pushed: 8 months ago - Stars: 31 - Forks: 8

deargen/mt-dti

An official Molecule Transformer Drug Target Interaction (MT-DTI) model

Language: Python - Size: 43 KB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 31 - Forks: 19

Pranavkhade/PACKMAN

PACKMAN: PACKing and Motion ANalysis

Language: Python - Size: 12.3 MB - Last synced: 23 days ago - Pushed: 4 months ago - Stars: 31 - Forks: 5

aws-samples/lm-gvp

LM-GVP: A Generalizable Deep Learning Framework for Protein Property Prediction from Sequence and Structure

Language: Jupyter Notebook - Size: 353 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 29 - Forks: 3

sacdallago/biotrainer

Language: Python - Size: 8.02 MB - Last synced: about 10 hours ago - Pushed: 11 days ago - Stars: 29 - Forks: 5

pierrepo/PBxplore

A suite of tools to explore protein structures with Protein Blocks :snake:

Language: Python - Size: 50.9 MB - Last synced: 19 days ago - Pushed: over 3 years ago - Stars: 28 - Forks: 17

jowoojun/biovec

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

Language: Python - Size: 179 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 26 - Forks: 8

food-nutrients/nutri-score

Nutri-Score Calculator - The goal of the project is to provide simple library that can calculate the Nutri-Score.

Language: JavaScript - Size: 882 KB - Last synced: 7 days ago - Pushed: over 1 year ago - Stars: 26 - Forks: 6

sanderlab/alignmentviewer

Multiple sequence alignment visualizer

Language: JavaScript - Size: 9.26 MB - Last synced: 2 days ago - Pushed: over 1 year ago - Stars: 25 - Forks: 6

TurtleTools/caretta

A software-suite to perform multiple protein structure alignment and structure feature extraction.

Language: Python - Size: 22.5 MB - Last synced: 5 days ago - Pushed: 9 months ago - Stars: 25 - Forks: 4

wrf/pdbcolor

Python code to color a PDB structure based on parameters from a multiple sequence alignment

Language: Python - Size: 15.4 MB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 24 - Forks: 5

lightdock/lightdock-python2.7

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

Language: C++ - Size: 64 MB - Last synced: 8 months ago - Pushed: about 4 years ago - Stars: 24 - Forks: 9

iquasere/reCOGnizer

A tool for domain based annotation with databases from the Conserved Domains Database

Language: HTML - Size: 61.3 MB - Last synced: about 1 month ago - Pushed: 5 months ago - Stars: 24 - Forks: 2

hkmztrk/SMILESVecProteinRepresentation

Language: Python - Size: 15.6 MB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 24 - Forks: 15

lightdock/lightdock-rust

A Rust implementation of the LightDock macromolecular docking software

Language: Rust - Size: 10.5 MB - Last synced: 25 days ago - Pushed: 26 days ago - Stars: 23 - Forks: 5

NYXFLOWER/TIP

TIP: Tri-graph Interaction Propagation model for Polypharmacy Side Eﬀect Prediction (GRL@NeurIPS, 2019)

Language: Python - Size: 294 MB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 23 - Forks: 15

DeepGraphLearning/esm-s

Structure-Informed Protein Language Model

Language: Python - Size: 928 KB - Last synced: 10 days ago - Pushed: 3 months ago - Stars: 23 - Forks: 3

dohlee/antiberty-pytorch

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

Language: Jupyter Notebook - Size: 228 KB - Last synced: 24 days ago - Pushed: about 2 months ago - Stars: 22 - Forks: 5

RedesignScience/AlphaSpace2

Protein surface topographical mapping tool

Language: Jupyter Notebook - Size: 22.4 MB - Last synced: 8 days ago - Pushed: 9 months ago - Stars: 21 - Forks: 5

matteoferla/MichelaNGLo-app

A web app to convert a PyMOL PSE file or PDB file to a easy to implement NGL.js view that can be implemented easily on any site

Language: Mako - Size: 107 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 21 - Forks: 4

310-ai/lib310

lib310 python package

Language: C++ - Size: 566 KB - Last synced: about 2 months ago - Pushed: 12 months ago - Stars: 21 - Forks: 2

HySonLab/Protein_Redesign

Complex-based Ligand-Binding Proteins Redesign by Equivariant Diffusion-based Generative Models

Language: Python - Size: 831 KB - Last synced: about 10 hours ago - Pushed: 1 day ago - Stars: 21 - Forks: 1

bayer-science-for-a-better-life/topefind-public

Finding the pitfalls of deep learning predictors of interacting residues in antibodies 🦠

Language: Python - Size: 42.9 MB - Last synced: 17 days ago - Pushed: 3 months ago - Stars: 20 - Forks: 0

medbioinf/pia

:books: :microscope: PIA - Protein Inference Algorithms

Language: Java - Size: 49.5 MB - Last synced: 22 days ago - Pushed: 5 months ago - Stars: 20 - Forks: 9

google-deepmind/nuclease_design

ML-guided enzyme engineering

Language: Jupyter Notebook - Size: 30.6 MB - Last synced: 22 days ago - Pushed: 22 days ago - Stars: 20 - Forks: 3

leeyang/ResPRE

ResPRE is an algorithm for protein residue-residue contact-map prediction

Language: Python - Size: 58 MB - Last synced: 7 months ago - Pushed: almost 5 years ago - Stars: 20 - Forks: 8

ProteinQure/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.

Language: Python - Size: 83.3 MB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 20 - Forks: 24

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.

Language: C++ - Size: 8.42 MB - Last synced: 11 days ago - Pushed: 4 months ago - Stars: 18 - Forks: 1

Related Keywords

protein 464 bioinformatics 118 protein-structure 89 python 59 dna 46 deep-learning 34 pdb 31 structural-biology 29 biology 28 machine-learning 26 rna 26 protein-sequences 24 proteomics 21 structure 19 pytorch 19 computational-biology 18 protein-design 18 visualization 16 fasta 15 protein-protein-interaction 14 protein-sequence 14 genomics 14 python3 13 amino-acids 13 molecular-dynamics 12 sequence 12 proteins 11 drug-discovery 10 transformer 10 pymol 10 prediction 10 mass-spectrometry 10 tensorflow 9 dna-sequences 9 artificial-intelligence 9 bioinformatics-tool 9 docking 9 peptides 9 r 9 database 9 simulation 9 alignment 9 ligand 8 osp-model 8 protein-structure-prediction 8 pk-sim 8 pdb-files 8 pbpk 8 javascript 8 molecule 8 classification 8 protein-data-bank 8 nutrition 7 molecular-biology 7 graph-neural-networks 7 chemistry 7 conservation 7 biopython 7 dataset 7 clustering 7 science 7 jupyter-notebook 7 biotechnology 6 translation 6 blast 6 nucleotides 6 graph-neural-network 6 genetics 6 bioinformatics-pipeline 6 genome 6 protein-language-model 6 protein-function-prediction 6 nlp 6 sequence-alignment 6 drug 6 uniprot 6 graph 6 webserver 5 cpp 5 rust 5 generative-model 5 lstm 5 neural-network 5 protein-ligand-interactions 5 keras 5 annotation 5 nucleotide 5 food 5 peptide 5 java 5 structural-bioinformatics 5 interaction 5 data-science 5 genes 5 plot 5 language-model 5 molecular-dynamics-simulation 5 research 4 algorithms 4 biochemistry 4