Projects in Awesome Lists tagged with structural-bioinformatics
A curated list of projects in awesome lists tagged with structural-bioinformatics .
https://github.com/biojava/biojava
:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
bioinformatics genomics java parser-library pdb protein-data-bank protein-modification protein-sequences protein-structure sequence-alignment structural-bioinformatics structure-alignment
Last synced: 17 Dec 2025
https://github.com/haddocking/pdb-tools
A dependency-free cross-platform swiss army knife for PDB files.
bioinformatics pdb protein python rcsb structural-bioinformatics structural-biology utrecht-university
Last synced: 10 Jan 2026
https://github.com/juliamolsim/molly.jl
Molecular simulation in Julia
julia lennard-jones molecular-dynamics molecular-simulation physics-simulation protein-structure structural-bioinformatics
Last synced: 15 May 2025
https://github.com/rdk/p2rank
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.
binding-sites bioinformatics drug-discovery groovy java ligand machine-learning mmcif molecular-structures p2rank pdb protein-ligand-docking protein-ligand-interactions protein-structure protein-surface proteins pymol random-forest structural-bioinformatics virtual-screening
Last synced: 12 Apr 2025
https://github.com/BioJulia/BioStructures.jl
A Julia package to read, write and manipulate macromolecular structures
bioinformatics biojulia biology julia pdb protein-structure structural-bioinformatics structural-biology
Last synced: 22 Jul 2025
https://github.com/biojulia/biostructures.jl
A Julia package to read, write and manipulate macromolecular structures
bioinformatics biojulia biology julia pdb protein-structure structural-bioinformatics structural-biology
Last synced: 30 Jan 2026
https://github.com/diegozea/mitos.jl
A Julia package to analyze protein sequences, structures, and evolutionary information
bioinformatics biology coevolution conservation julia-language multiple-sequence-alignment mutual-information pdb pfam protein-evolution protein-sequence-analysis protein-structure proteins sifts structural-bioinformatics
Last synced: 05 Apr 2025
https://github.com/mooerslab/pymolshortcuts
The repository pymolschortucts contains the a collection of shortcuts that are loaded on startup of PyMOL. These shortcuts enable websearches from within PyMOL as well as many other convienent functions that make work in PyMOL more productive..
agile-programming agile-pymol aliases biomolecular-artwork efficient-programming ergonomic-keyword-use figure-making image-making molecular-artwork molecular-graphics pdb pml protein-structure-analysis pymol pymol-plugin pymol-python scripting shortcuts startup-script structural-bioinformatics
Last synced: 16 Mar 2026
https://github.com/carlocamilloni/structural-bioinformatics
This repository includes the slides and the practicals for the course of Structural Bioinformatics of the MBB/QB degrees at the University of Milano, originally inspired by https://github.com/pb3lab/ibm3202
docking molecular-dynamics structural-bioinformatics structural-biology structure-prediction teaching-materials
Last synced: 19 Aug 2025
https://github.com/jgreener64/pdb-benchmarks
Benchmarking common tasks on proteins in various languages and packages
benchmarks bioinformatics comparison mmcif mmtf pdb pdb-files structural-bioinformatics
Last synced: 11 Apr 2025
https://github.com/jgreener64/bio3dview.jl
A Julia package to view macromolecular structures in the REPL, in a Jupyter notebook/JupyterLab or in Pluto
bioinformatics ijulia julia jupyter-notebook pluto protein-structure structural-bioinformatics structural-biology
Last synced: 23 Oct 2025
https://github.com/samirelanduk/molstar-react
Molstar as a react component
bioinformatics molstar pdb protein-visualization react structural-bioinformatics
Last synced: 03 Mar 2025
https://github.com/n-szulc/fingernat
Software for detecting non-covalent interactions formed within complexes of nucleic acids with ligands.
bioinformatics bioinformatics-tool dna drug-target-interactions interactions ligand-complex ligand-receptor-interaction ligand-target molecular-interactions nucleic-acids rna rna-ligand-complexes scientific-computing structural-bioinformatics structural-interaction-fingerprint
Last synced: 26 Oct 2025
https://github.com/jgreener64/proteinensembles.jl
Generate and perturb protein structural ensembles using the ExProSE algorithm
allosteric-predictions allostery coarse-grained julia paper protein-structure structural-bioinformatics
Last synced: 11 Apr 2025
https://github.com/mooerslab/easypymol
Script to facilitate the making of horizontal scripts
ambient-occulsion biomolecular-structures black-and-white-cartoons coordinate-covalent-bonds horizontal-scripts metal-coordination molecular-artwork molecular-graphics molecular-structures molecular-visuallization pml protein-structure pymol pymol-macro-language rna-structure roundview scripting startup-aliases structural-bioinformatics tutorial-videos
Last synced: 08 May 2025
https://github.com/pdbeurope/protein-cluster-conformers
Clusters protein chains based on CA distance difference
bioinformatics bioinformatics-tool clustering conformal-prediction conformational-state pdb protein-structure proteins structural-bioinformatics structural-biology superposition
Last synced: 25 Jul 2025
https://github.com/Sarah-Hesham-2022/Unity-Protein-Visualization
Protein Visualization using Unity and C# analysis on PDB Files.
bioinformatics csharp file-analysis pdb-files problem-solving protein-structure structural-bioinformatics structural-biology unity visualization
Last synced: 19 Apr 2025
https://github.com/deeprank/ponder
PointNet for Deep Rank: protein-protein interaction scoring using neural networks
deep-learning pdb point-cloud pointnet protein-protein-interaction structural-bioinformatics
Last synced: 14 Feb 2026
https://github.com/tawssie/zmpy3d
Python implementation of 3D Zernike moments with NumPy
3d-zernike numpy protein-structure python structural-bioinformatics superposition zernike-moments
Last synced: 15 Apr 2025
https://github.com/rsanchezgarc/bipspi
Partner specific prediction of protein binding sites
bioinformatics machine-learning protein-protein-interaction proteins structural-bioinformatics
Last synced: 10 Apr 2025
https://github.com/jewettaij/dlpdb
collect statistics from the entire PDB library
pdb-files structural-bioinformatics
Last synced: 18 Jan 2026
https://github.com/tawssie/zmpy3d_cp
Python implementation of 3D Zernike moments with CuPy
3d-zernike cuda cupy gpu protein-structure python structural-bioinformatics superposition zernike-moments
Last synced: 15 Apr 2025
https://github.com/tawssie/zmpy3d_tf
Python implementation of 3D Zernike moments with Tensorflow
3d-zernike gpu protein-structure python structural-bioinformatics superposition tensorflow zernike-moments
Last synced: 15 Apr 2025
https://github.com/drewschaub/protein-design-tools
A library of tools for protein design
protein-design structural-bioinformatics
Last synced: 16 Jan 2026
https://github.com/tawssie/zmpy3d_pt
Python implementation of 3D Zernike moments with PyTorch
3d-zernike cuda gpu protein-structure python pytorch structural-bioinformatics superposition zernike-moments
Last synced: 24 Oct 2025
https://github.com/babaid/probindnn
My bachelors thesis on predicting relative protein-protein binding affinity changes upon point mutations using graph neural networks.
bioinformatics biophysics deep-learning graph-neural-networks graphs lstm lstm-neural-networks neural-networks physics pytorch pytorch-geometric structural-bioinformatics
Last synced: 17 May 2026
https://github.com/giatraskon/algorithms-in-structural-bioinformatics-assignments
Assignments from the 'Algorithms in Structural Bioinformatics' graduate course, exploring RNA folding, molecular conformational analysis, and protein structure comparison using Python and bioinformatics tools.
alphafold2 bioinformatics biopython chimerax computational-biology conformational-analysis crude-energy-minimization jupyter-notebook protein-structure-analysis pymol python rmsd rna-folding root-mean-square-deviation sars-cov-2 secondary-structure-elements serotonin structural-bioinformatics structural-biology structure-visualization
Last synced: 22 Apr 2026
https://github.com/elkins/synth-pdb
Generate realistic PDB files with mixed secondary structures for testing, education and bioinformatics tool development
amino-acid-sequence bioinformatics biophysics computational-structural-biology molecular-modeling nmr-spectroscopy nmr-tools peptide peptide-sequences protein protein-data-bank protein-structure ramachandran science-education scientific-computing secondary-structure simulation structural-bioinformatics structural-biology
Last synced: 03 Jun 2026
https://github.com/madsondeluna/bits_bytes_biomolecules
Modelagem por Deep Learning, Threading, Ab initio ou Homologia? Antes de escolher o método, entenda como a termodinâmica e a evolução conduzem o dobramento proteico. Um curso focado em tomar decisões sobre quando e como utilizar cada abordagem, com base na hipótese e nos dados disponíveis.
bioinformatics college-project short-course structural-bioinformatics structural-biology
Last synced: 03 May 2026
https://github.com/babaid/aaperturb
A C++ library for the creation of a large dataset of amino acid sidechain perturbations, own PDB Parser code included and some other things related.
big-data gnn molecular-dynamics perturbation-methods structural-bioinformatics
Last synced: 10 Jun 2025
https://github.com/madsondeluna/alaninescanning4eif4e
A Python framework for computational alanine scanning and hotspot identification using Rosetta's Flex ddG protocol.
alanine-scanning mutation-analysis protein-stability rosetta-scripts structural-bioinformatics
Last synced: 03 May 2026