63 Open Source Protein Software Projects

Official git repository for Biopython (originally converted from CVS)

Efficient pythonic random access to fasta subsequences

Ribbon diagrams of proteins in #golang.

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

A Python Package for Protein Dynamics Analysis

Bio4j abstract model and general entry point to the project

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

Protein Graph Library

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

Evolutionary couplings from protein and RNA sequence alignments

Protein-compound affinity prediction through unified RNN-CNN

Inclusive model of expression dynamics with metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses

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

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

View proteins and trajectories in the terminal

ProteinGCN: Protein model quality assessment using Graph Convolutional Networks

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.

Python package to annotate and visualize gene fusions.

Protein structure comparison tools such as SSAP and SNAP

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

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

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

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

:books: :microscope: PIA - Protein Inference Algorithms

:fork_and_knife: Food Nutrients

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

:microscope: Train an Amino Acid Embeddings (or a dragon?)

MerCat: python code for versatile k-mer counting and diversity estimation for database independent property analysis for meta -ome data

BLAST Sequence Searches with R

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

waka waka

Web application for protein-ligand binding sites analysis and visualization

PyTorch implementations of protein secondary structure prediction on CB513.

This program dereplicates and/or filter nucleotide and/or protein database from a list of names or sequences (by exact match).

Guided Conditional Wasserstein GAN for De Novo Protein Design

A Python package for extracting protein sequence features

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.

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

🧬 An R package for visualizing molecular data in 3D

Differentiable molecular simulation of proteins with a coarse-grained potential

Fast and flexible ORF finder

Protein cavity identification and automatic subpocket decomposition

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

Neural Networks for Protein Sequence Alignment

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.

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

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

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

TIP: Tri-graph Interaction Propagation model for Polypharmacy Side Effect Prediction ([email protected], 2019)

Graph Network for protein-protein interface

Multiple sequence alignment visualizer

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

☢️ Reverse engineering the poliovirus.

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

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

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

Protein surface topographical mapping tool

PCA and normal mode analysis of proteins

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

VSCode Extension for interactively visualising protein structure data in the editor

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

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