Ecosyste.ms: Repos

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

GitHub topics: protein

Repositories

MurrellGroup/ProtPlot.jl

Protein ribbon plots implemented in Julia using GLMakie

Language: Julia - Size: 1.36 MB - Last synced: about 3 hours ago - Pushed: about 3 hours ago - Stars: 8 - Forks: 1

bigbio/pgt-pangenome

Protegenomics analysis based on Pangenome references

Language: Jupyter Notebook - Size: 574 MB - Last synced: about 4 hours ago - Pushed: about 4 hours ago - Stars: 0 - Forks: 0

SPC-Facility-EMBL-Hamburg/eSPC_biophysics_platform

A collection of tools to analyse biophysical data. Written mostly in R and Python.

Language: R - Size: 39.2 MB - Last synced: about 7 hours ago - Pushed: 1 day ago - Stars: 2 - Forks: 0

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

HySonLab/Protein_Redesign

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

Language: Python - Size: 831 KB - Last synced: about 11 hours ago - Pushed: 1 day ago - Stars: 21 - Forks: 1

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

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

westlake-repl/ProteinLM-TDG2-Mutation

Protein language models-assisted optimization of a uracil-N-glycosylase variant enables programmable T-to-G and T-to-C base editing

Language: Jupyter Notebook - Size: 7.8 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 9 - Forks: 0

diaas-calculator/diaas-calculator-angular

Angular frontend for the protein DIAAS calculator

Language: TypeScript - Size: 169 KB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 0 - Forks: 0

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

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

tyang816/ProtSSN

Fusion of protein sequence and structural information, using denoising pre-training network for protein engineering (zero-shot).

Language: Python - Size: 28.4 MB - Last synced: 3 days ago - Pushed: 4 days ago - Stars: 17 - Forks: 0

naity/protein-transformer

Implement, train, tune, and evaluate a transformer model for antibody classification with this step-by-step code.

Language: Jupyter Notebook - Size: 22.9 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 2 - Forks: 2

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

raimondilab/precogx

A predictor of GPCR couplings with G-proteins/B-arrs using Transformers

Language: JavaScript - Size: 2.21 GB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 6 - Forks: 2

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

diaas-calculator/diaas-calculator-rust

Backend for the protein DIAAS calculator

Language: Rust - Size: 39.1 KB - Last synced: 4 days ago - Pushed: 5 days ago - Stars: 0 - Forks: 0

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

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

hfswetton/PDBCor Fork of dzmitryashkinadze/PDBCor

Extraction of correlations from multistate PDB protein coordinates

Language: Python - Size: 11.7 MB - Last synced: 4 days ago - Pushed: 5 days ago - Stars: 0 - Forks: 0

wells-wood-research/de-stress

DE-STRESS is a model evaluation pipeline that aims to make protein design more reliable and accessible.

Language: Elm - Size: 21.9 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 15 - Forks: 1

MooersLab/colabpymolpysnips

Library of PyMOL Python snippets for Google Colab.

Language: Jupyter Notebook - Size: 2.41 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 3 - Forks: 7

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

MurrellGroup/Backboner.jl

Types and utilities for handling backbones

Language: Julia - Size: 1.07 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 2 - Forks: 1

Jon-Ting/covdrugsim

:zap: A package to automate quantum mechanical calculations and molecular dynamics simulations of drugs.

Language: Python - Size: 2.58 MB - Last synced: 8 days ago - Pushed: 9 days ago - Stars: 1 - Forks: 0

bioinfodlsu/phage-host-prediction

Published in PLOS ONE. Phage-host interaction prediction tool that uses protein language models to represent the receptor-binding proteins of phages. It presents improvements over using handcrafted sequence properties and eliminates the need to manually extract and select features from phage sequences

Language: Jupyter Notebook - Size: 10.9 MB - Last synced: 9 days ago - Pushed: 10 days ago - Stars: 9 - Forks: 2

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

Fraternalilab/POPScomp

Solvent Accessible Surface Areas of Biomolecules and their Complexes

Language: C - Size: 5.97 MB - Last synced: 10 days ago - Pushed: 11 days ago - Stars: 14 - Forks: 3

raw-lab/mercat2

MerCat2: python code for versatile k-mer counting and diversity estimation for database independent property analysis for metaome data

Language: HTML - Size: 105 MB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 8 - Forks: 1

sacdallago/biotrainer

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

aws-samples/sagemaker-documentdb-train-gnn-for-millions-proteins

Training graph neural nets for millions of proteins on Amazon SageMaker and DocumentDB.

Language: Jupyter Notebook - Size: 341 KB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 5 - Forks: 2

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

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

NutrientInstitute/protein-digestibility

Protein Digestibility Data

Language: R - Size: 1.88 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 0 - Forks: 0

gdocking/gdock

Protein-Protein Docking using Genetic Algorithm

Language: Python - Size: 6.65 MB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 14 - Forks: 2

hshadman/2d_conformational_landscape_map

Use PyConforMap to generate a simple scatter plot to map conformational landscapes of intrinsically disordered proteins, and quantify conformational diversity.

Language: Jupyter Notebook - Size: 23.4 MB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 0 - Forks: 0

Croydon-Brixton/proteinmpnn_wrapper

A thin wrapper around ProteinMPNN for convenient sampling without having to write out or consume files

Language: Python - Size: 82 MB - Last synced: 2 days ago - Pushed: 16 days ago - Stars: 6 - Forks: 0

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

Kitaolab/PaCS-Toolkit

PaCS-Toolkit: Optimized software utilities for PaCS-MD and following analysis

Language: Python - Size: 1.93 MB - Last synced: 19 days ago - Pushed: 19 days ago - Stars: 2 - Forks: 1

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

FZJ-JSC/speadi

A Python package that aims to characterise the dynamics of local chemical environments from Molecular Dynamics trajectories of proteins and other biomolecules. Public mirror of https://gitlab.jsc.fz-juelich.de/slbio/speadi.

Language: Python - Size: 1.02 MB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 6 - Forks: 0

0xnu/nwunsch_lua

Needleman–Wunsch algorithm implementation in Lua.

Language: Lua - Size: 30.3 KB - Last synced: 14 days ago - Pushed: 21 days ago - Stars: 0 - Forks: 0

MurrellGroup/AssigningSecondaryStructure.jl

Simplified DSSP algorithm implemented in native Julia

Language: Julia - Size: 242 KB - Last synced: 21 days ago - Pushed: 21 days ago - Stars: 1 - Forks: 0

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

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

ProteinDF/ProteinDF

Canonical (Kohn-Sham) molecular orbital calculation software for large molecules such as protein

Language: C++ - Size: 36.8 MB - Last synced: 23 days ago - Pushed: 23 days ago - Stars: 12 - Forks: 5

pgarrett-scripps/peptacular

A spectacularly simple package for working with peptide sequences.

Language: Python - Size: 11.3 MB - Last synced: 24 days ago - Pushed: 25 days ago - Stars: 8 - Forks: 0

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 11 hours ago - Pushed: 26 days ago - Stars: 153 - Forks: 13

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

MolBioMedUAB/EMDA

Python package for easy analysis of MD simulations based on MDAnalysis.

Language: Jupyter Notebook - Size: 13.4 MB - Last synced: 26 days ago - Pushed: 26 days ago - Stars: 0 - Forks: 0

UnixJunkie/MMO

Molecular Mechanics in OCaml

Language: OCaml - Size: 1.46 MB - Last synced: 27 days ago - Pushed: 27 days ago - Stars: 1 - Forks: 0

futianfan/GenoCraft

GenoCraft: A Comprehensive, User-Friendly Web-Based Platform for High-Throughput Omics Data Analysis and Visualization

Language: SCSS - Size: 68.2 MB - Last synced: 14 days ago - Pushed: 27 days ago - Stars: 13 - Forks: 0

0xnu/nwunsch

Needleman–Wunsch algorithm implementation in Go.

Language: Go - Size: 12.7 KB - Last synced: 14 days ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

PixelgenTechnologies/pixelator

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

Language: Python - Size: 36 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 9 - Forks: 1

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

ugSUBMARINE/shortest-path

Find shortest path between selected residues in a protein structure

Language: Python - Size: 1.23 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

grimmlab/ProLaTherm

Protein Language Model-based Protein Thermophilicity Prediction

Language: Python - Size: 27.6 MB - Last synced: 4 days ago - Pushed: about 1 month ago - Stars: 2 - Forks: 0

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

ninnii55/Amino_align

Python code for bioinformatics about proteins

Language: Jupyter Notebook - Size: 2.88 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

Jiadong001/AI4Bio_Paper_Reading_List

List of latest/classical papers about AI for Biology. Beginning in 2023. Present emphasis on Protein.

Size: 2.28 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

pgarrett-scripps/ProteinCleaverStreamlitApp

Protein Cleaver is a versatile tool for protein analysis and digestion.

Language: Python - Size: 748 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 3 - Forks: 0

pgarrett-scripps/PeptideFragmenterStreamlitApp

A peptide fragment ion calculator made with streamlit

Language: Python - Size: 110 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 2 - Forks: 0

ebi-uniprot/uniprot-store

This project is for building uniprot search engine

Language: Java - Size: 11.6 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 3 - Forks: 0

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

abdulsalam-bande/swifty

This is a work to improve molecular docking speed. Normally docking a ligand on a target protein is done with some very complex functions and it is often slow. This work uses Neural Networks to model ligands on target proteins to measure whether they are active or not.

Language: Python - Size: 8.29 MB - Last synced: 24 days ago - Pushed: about 2 months ago - Stars: 1 - Forks: 0

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

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

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

ugSUBMARINE/psatm

Create pseudoatoms at the centroid of the catalytic atoms of a residue

Language: Rust - Size: 719 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

snijderlab/align-cli

A CLI for pairwise alignment of sequences, using both normal and mass based alignment.

Language: Rust - Size: 841 KB - Last synced: 27 days ago - Pushed: about 2 months ago - Stars: 6 - Forks: 0

strumenti-formali-per-la-bioinformatica/contrastive-3d-protein-prediction Fork of angelonazzaro/contrastive-3d-protein-prediction

[a.a. 23/24] A. Nazzaro, L. Costante

Language: Python - Size: 57.1 MB - Last synced: 22 days ago - Pushed: 2 months ago - Stars: 1 - Forks: 0

angelonazzaro/contrastive-3d-protein-prediction

A contrastive approach for 3d protein prediction.

Language: Python - Size: 57.1 MB - Last synced: 22 days ago - Pushed: 2 months ago - Stars: 1 - Forks: 2

lzillich/LIS1_code

Zillich, Rossetti, Fechtner et al. (2023)

Language: R - Size: 73.2 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

xnought/protein-scatter

Visualizing 3D fragments of proteins in a scatterplot

Language: Jupyter Notebook - Size: 1.77 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

riquri/wheel-diagram

Plot wheel diagram for alpha-helix.

Language: HTML - Size: 261 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 3 - Forks: 0

chao1224/ProteinDT

Language: Python - Size: 19.3 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 14 - Forks: 0

huiwenke/MineProt

Stand-alone server for structural proteome curation

Language: PHP - Size: 5.95 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 5 - Forks: 0

ahabegger/CA-2-HCOMB

CA-2-HCOMB is a tool for simplifying single-chain protein structures from PDB files into manageable models like various honeycombs, retaining essential information for in-depth computations. It's efficient for large datasets and machine learning, and user-friendly for research and education.

Language: Python - Size: 2.12 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 1 - Forks: 0

pallucs/PTMGPT2

GPT-based protein language model for PTM site prediction

Language: Jupyter Notebook - Size: 1.62 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

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

ahabegger/HCOMB-2-CA

Lattice2Backbone is a software tool that converts lattice representations of protein structures into detailed, carbon alpha-only backbone structures, bridging the gap between simplified models and comprehensive biological analysis in structural biology and bioinformatics.

Language: Python - Size: 32.2 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 1 - Forks: 0

derekmichaelwright/AGILE_LDP_Protein

Evaluating the breeding potential of cultivated lentils for protein and amino acid content and quality

Language: HTML - Size: 862 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 1

Fluorescence-Tools/chisurf

Global analysis platform for fluorescence data

Language: Python - Size: 193 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 12 - Forks: 1

abhijitju06/JUMPt-Version-1.0.0

JUMPt Version 1.0.0

Language: MATLAB - Size: 1.95 MB - Last synced: 22 days ago - Pushed: 3 months ago - Stars: 1 - Forks: 0

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

gozsari/ProtFeat

ProtFeat is protein feature extraction tool that utilizes POSSUM and iFeature.

Language: Python - Size: 125 MB - Last synced: about 21 hours ago - Pushed: 3 months ago - Stars: 15 - Forks: 0

Lakshanj98/Distinguish-Sequence-Type_Transcription_Translation

Distinguishes the sequence type. Transcribe the DNA to RNA. Translate the RNA to Protein.

Language: Python - Size: 3.91 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

pendy05/vDiveR_RShiny

viral protein Diversity dynamics Visualization in R (vDiveR; https://protocol-viral-diversity.shinyapps.io/vDiveR/)

Language: R - Size: 4.54 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 1 - Forks: 0

Jeshuwin/rcsbmass

rcsbmass: simplifies downloading Protein Data Bank (PDB) files by automating bulk downloads with customizable JSON-based queries. Ideal for researchers needing large datasets.

Language: Jupyter Notebook - Size: 1.36 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

barel-mishal/Beilinson-NutriGoalCalc-

NutriGoalCalc: A simple app for personalized nutrition planning. Calculate your caloric, and protein, needs easily, based on your health metrics. Ideal for both individuals and healthcare professionals.

Language: TypeScript - Size: 49.8 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0