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Jolecule ⭐ 48

Javascript viewer for proteins and DNA with animated views

Deeprank Gnn ⭐ 48

Graph Network for protein-protein interface

Bioblender21 ⭐ 47

Blender plugin to process biological data and molecular work.

Protein Interface Prediction using Graph Convolutional Networks

Proteingcn ⭐ 47

ProteinGCN: Protein model quality assessment using Graph Convolutional Networks

Gnn_dove ⭐ 47

Code for "Protein Docking Model Evaluation by Graph Neural Networks"

Protein Atlas Fastai ⭐ 46

Code for training a Resnet model for the Human Protein Atlas Image Classification competition

Agfusion ⭐ 46

Python package to annotate and visualize gene fusions.

View proteins and trajectories in the terminal

Oncoenrichr ⭐ 46

Cancer-dedicated gene set interpretation

Deepdrug3d ⭐ 46

A convolutional neural network for classifying binding pockets based on spatial and chemical information extracted from the pockets.

Repository for student projects within biomedical text mining from Lund University

iLearn, a Python Toolkit and Web Server Integrating the Functionality of Feature Calculation, Extraction, Clustering, Feature Selection, Feature Normalization, Dimension Reduction and Model Construction for Classification, Best Model Selection, Ensemble Learning and Result Visualization for DNA, RNA and Protein Sequences.

Sequence_manipulation_suite ⭐ 45

A collection of simple JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. The Sequence Manipulation Suite is commonly used by molecular biologists, for teaching purposes, and for program and algorithm testing.

Function prediction using a deep ontology-aware classifier

Prothint ⭐ 45

Protein hint generation pipeline for gene finding in eukaryotic genomes

Ensembler ⭐ 44

Automated omics-scale protein modeling and simulation setup.

Paired_cell_inpainting ⭐ 44

Self-supervised learning for microscopy images

Vae_protein_function ⭐ 44

Protein function prediction using a variational autoencoder

Cell2cell ⭐ 44

User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins

Trdesign ⭐ 44

trRosetta for protein design

Deepconv Dti ⭐ 43

DeepConv-DTI: Prediction of drug-target interactions via deep learning with convolution on protein sequences

Fluentdna ⭐ 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.

Protein Localization ⭐ 43

Using Transformer protein embeddings with a linear attention mechanism to make SOTA de-novo predictions for the subcellular location of proteins 🔬

RxDock is a fork of rDock. Note: the latest code is under development. Please do git checkout patched-rdock after clone if you want patched rDock. [IMPORTANT NOTE: pull requests should be posted on GitLab, this is a read-only source code mirror]

Prismnet ⭐ 41

Predicting dynamic cellular protein-RNA interactions using deep learning and in vivo RNA structure

Pfeature ⭐ 41

A software package for computing features of peptides and proteins

Sequence Viewer ⭐ 41

neXtProt protein sequence viewer (javascript) - From SIB CALIPHO group; neXtProt project

Drugmechdb ⭐ 41

A database of paths that represent the mechanism of action from a drug to a disease in an indication.

Peptide Shaker ⭐ 41

Interpretation of proteomics identification results

Microbeannotator ⭐ 41

Pipeline for metabolic annotation of microbial genomes

Normalize CITEseq Data

Protein Calculator ⭐ 40

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/

MD trajectory analysis using protein-ligand Interaction Fingerprints

Deepaccnet ⭐ 40

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

Smina Docking Benchmark ⭐ 40

Deepmind Alphafold Repl ⭐ 40

https://github.com/deepmind/deepmind-research

Open Source Protein REdesign for You v3

Protocolgromacs ⭐ 40

Automatic gromacs protocol from preparation to production with ligand parametrization through

Machine Learning With Ontologies ⭐ 39

Force Fields ⭐ 39

Protlearn ⭐ 38

A Python package for extracting protein sequence features

Macsyfinder ⭐ 38

MacSyFinder - Detection of macromolecular systems in protein datasets using systems modelling and similarity search.

R package for Protein activity analysis of single-cell RNAseq.

Megadock ⭐ 38

An ultra-high-performance protein-protein docking for heterogeneous supercomputers

A python toolkit for analysing membrane protein-lipid interactions.

ProFET: Protein Feature Engineering Toolkit for Machine Learning

Holoprot ⭐ 37

Multi-Scale Representation Learning on Proteins (NeurIPS 2021)

Fahclient ⭐ 36

Dockerized Folding@home client with NVIDIA GPU support to help battle COVID-19

R package for analysing proteomics data

Implementation and replication of ProGen, Language Modeling for Protein Generation, in Jax

Associative memory, Water mediated, Structure and Energy Model (AWSEM) protein simulation code

Differentiable molecular simulation of proteins with a coarse-grained potential

Localpdb ⭐ 36

Python package to manage protein structures and their annotations

Hmmer2go ⭐ 36

Annotate DNA sequences for Gene Ontology terms

Peptides.py ⭐ 36

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

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

Amazon Sagemaker Protein Classification ⭐ 35

Implementation of Protein Classification based on subcellular localization using ProtBert(Rostlab/prot_bert_bfd_localization) model from Hugging Face library, based on BERT model trained on large corpus of protein sequences.

Dips Plus ⭐ 34

The Enhanced Database of Interacting Protein Structures for Interface Prediction

The pmartR R package provides functionality for quality control, normalization, exploratory data analysis, and statistical analysis of mass spectrometry (MS) omics data, in particular proteomic (either at the peptide or the protein level), lipidomic, and metabolomic data.

Flu Sequence Predictor ⭐ 34

An experimental deep learning & genotype network-based system for predicting new influenza protein sequences.

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

GUI Components for (Java) Swing

Algorithm for Open Data Detection in Publications (ODDPub)

Timed Design ⭐ 34

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

Rcsb Saguaro ⭐ 34

1D Feature Viewer

Deepgoplus ⭐ 34

DeepGO with GOPlus axioms

Deepinteract ⭐ 33

A geometric deep learning pipeline for predicting protein interface contacts.

Graphsol ⭐ 33

Code of our JC paper: "Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map"

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

Deep Proteomics ⭐ 33

Hotspot3d ⭐ 33

3D hotspot mutation proximity analysis tool

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

Omnipath ⭐ 32

Python client for the OmniPath web service

Food Nutrients ⭐ 32

🍴 Food Nutrients

Protwis is the backbone of the GPCRdb. The GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs).

DLSCORE: A deep learning based scoring function for predicting protein-ligand binding affinity

Preforms De novo protein design using machine learning and PyRosetta to generate a novel protein structure

Deepdrug ⭐ 31

DeepDrug: A general graph-based deep learning framework for drug relation prediction

Babelomics ⭐ 31

Gromacs_ff ⭐ 31

Trusted force field files for gromacs

Meta-Omics Software for Community Analysis

Ribosome Binding Site Calculator V1.0 ⭐ 31

The Ribosome Binding Site (RBS) Calculator can predict the translation initiation rate of a protein coding sequence in bacteria and design synthetic RBS sequences to rationally control the translation initiation rate. It is used to design synthetic biological systems.

Subcellular_localization ⭐ 30

Because snacking shouldn't hurt your fat intake

Open source biolab

Biozernike ⭐ 30

Protein structure descriptors and alignment based on 3D Zernike moments.

Eukaryotic Non-Model Transcriptome Annotation Pipeline - Latest Release v1.0.1

Gopredsim ⭐ 29

Visually explore covariation in protein families

Biomedical Nlp Corpus ⭐ 29

Corpus (datasets) collection about biology and medical NLP.

Docker Foldingathome ⭐ 29

Omicsintegrator ⭐ 29

This repository is the working directory for the Garnet-Forest bundle of python scripts for analyzing diverse forms of 'omic' data in a network context.

INSert membrANE - A simple, versatile tool for building coarse-grained simulation systems

Fully convolutional neural networks for protein residue-residue contact prediction

Phylostratr ⭐ 28

An R framework for phylostratigraphy

Kaggle Human Protein Atlas Image Classification ⭐ 28

Kaggle 2018 @ Human Protein Atlas Image Classification

Fast, state-of-the-art ab initio prediction of protein secondary structure in 3 and 8 classes

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