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49 search results found

Biopython ⭐ 3,918

Official git repository for Biopython (originally converted from CVS)

Graphein ⭐ 932

Protein Graph Library

Biopandas ⭐ 673

Working with molecular structures in pandas DataFrames

Biojava ⭐ 564

📖🔬☕ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

Foldseek ⭐ 545

Foldseek enables fast and sensitive comparisons of large structure sets.

Hh Suite ⭐ 429

Remote protein homology detection suite.

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294

Lightdock ⭐ 234

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

P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.

Proteinflow ⭐ 151

Versatile computational pipeline for processing protein structure data for deep learning applications.

Foldcomp ⭐ 127

Compressing protein structures effectively with torsion angles

Biojava Tutorial ⭐ 111

📖📚An introductory tutorial for BioJava

Modelling the Language of Life - Deep Learning Protein Sequences

Biostructures.jl ⭐ 77

A Julia package to read, write and manipulate macromolecular structures (particularly proteins)

Mitos.jl ⭐ 64

Mutual Information Tools for protein Sequence analysis in Julia

PyMod 3 - sequence similarity searches, multiple sequence/structure alignments, and homology modeling within PyMOL.

The MPI Bioinformatics Toolkit

Awesome Structural Bioinformatics ⭐ 54

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.

The specification of the MMTF format for biological structures

Bio3dview.jl ⭐ 32

A Julia package to view macromolecular structures in the REPL, in a Jupyter notebook/JupyterLab or in Pluto

Manyfold ⭐ 28

🧬 ManyFold: An efficient and flexible library for training and validating protein folding models

Lightdock Python2.7 ⭐ 20

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

Voronota ⭐ 20

Voronota is a software tool for analyzing three-dimensional structures of biological macromolecules using the Voronoi diagram of atomic balls.

De Stress ⭐ 13

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

Lightdock Rust ⭐ 13

A Rust implementation of the LightDock macromolecular docking software

Proteinsolver ⭐ 12

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

Ramachandraw ⭐ 12

Ramachandran plotting tool

Alphafold Peptide Receptors ⭐ 11

Identifying peptide-receptor interactions using AlphaFold-Multimer

Cazy_webscraper ⭐ 10

Web scraper to retrieve protein data catalogued by the CAZy, UniProt, NCBI, GTDB and PDB websites/databases.

2D portraits of 3D protein structures

A bare metal Python library for building and manipulating protein molecular structures

🍃 SiNGA (Simulation of Natural Systems using Graph Automata) is an open-source library containing tools especially for structural bioinformatics and systems biology.

Protein Data Bank (pdb) file parser

Siteinterlock ⭐ 8

A toolkit for predicting the binding mode of small molecules interacting with proteins based on interfacial rigidification, as assessed by graph theoretic constraint counting on the covalent and noncovalent bond network. Raschka et al. (2016) Proteins: Structure, Function, and Bioinformatics

🔍 Fit3D - An application for template-based detection of small structural motifs in protein structures and macromolecular structure data.

Python_scripts ⭐ 7

scripts for parsing PDB, fasta, and GO

Aa_subtypes ⭐ 7

Code for the MSB publication: Exploring amino acid functions and positional subtypes in a deep mutational landscape

Surfstamp Public ⭐ 7

3D Printer Compatible Molecular Surface Representation (Do not clone! Everything is in the release page!)

Pdb2uniprot ⭐ 7

Convert PDB residues to their Uniprot equivalents

FTDMP is a software system for running docking experiments and scoring/ranking multimeric models.

Biojava Notebooks ⭐ 6

BioJava examples in Jupyter Notebooks

Exmachina ⭐ 6

Sequence aligner for accurate template-based protein structure prediction

Protein-Protein Docking using Genetic Algorithm

P2rank Framework ⭐ 6

The central entry point to the P2Rank project with links to the individual projects, including references to documentation, datasets, etc.

Unity Protein Visualization ⭐ 6

Protein Visualization using Unity and C# analysis on PDB Files.

Alphacutter ⭐ 6

This repository contains the AlphaCutter.py for the removal of non-globular regions from predicted protein structures.

Web server for automated modeling of loops in protein structures

Vizsnp St ⭐ 5

Visualizing the effect of SNPs on protein structure using iCn3D

Ps4 Dataset ⭐ 5

The largest open-source dataset for Protein Single Sequence Secondary Structure prediction.

Calculating a range of protein descriptors using their physicochemical, biological and structural properties 🔬.

a set of classes and submodules to build, manipulate and analyse three-dimensional protein structures.

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