GitHub topics: structural-bioinformatics
rdk/p2rank
P2Rank: Protein-ligand binding site prediction from protein structure based on machine learning.
Language: Groovy - Size: 676 MB - Last synced at: 1 day ago - Pushed at: about 1 month ago - Stars: 343 - Forks: 49
haddocking/pdb-tools
A dependency-free cross-platform swiss army knife for PDB files.
Language: Python - Size: 968 KB - Last synced at: 1 day ago - Pushed at: about 2 months ago - Stars: 427 - Forks: 117
harryjubb/arpeggio
Calculation of interatomic interactions in molecular structures
Language: Python - Size: 146 KB - Last synced at: 3 days ago - Pushed at: over 3 years ago - Stars: 79 - Forks: 24
haddocking/haddocking.github.io
Webpage of the Bonvinlab @ Utrecht University and HADDOCK software
Language: HTML - Size: 902 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 13 - Forks: 21
JuliaMolSim/Molly.jl
Molecular simulation in Julia
Language: Julia - Size: 88.2 MB - Last synced at: 2 days ago - Pushed at: 3 days ago - Stars: 444 - Forks: 58
diegozea/MIToS.jl
A Julia package to analyze protein sequences, structures, and evolutionary information
Language: Julia - Size: 60.9 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 83 - Forks: 16
amjjbonvin/haddocking.github.io Fork of haddocking/haddocking.github.io
Webpage of the HADDOCK group
Language: HTML - Size: 890 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 0 - Forks: 0
lightdock/lightdock
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
Language: Python - Size: 93.4 MB - Last synced at: 2 days ago - Pushed at: 2 months ago - Stars: 353 - Forks: 47
BioJulia/BioStructures.jl
A Julia package to read, write and manipulate macromolecular structures
Language: Julia - Size: 12.1 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 105 - Forks: 25
biojava/biojava
:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
Language: Java - Size: 48.8 MB - Last synced at: 2 days ago - Pushed at: about 2 months ago - Stars: 613 - Forks: 390
CBFLivUni/Leptospira-LIC13259-C8G
Code to reproduce work in paper titled 'AlphaFold reveals how pathogenic Leptospira use thiol-disulphide exchange to evade the complement membrane attack complex'
Language: Shell - Size: 405 KB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 0 - Forks: 0
jgreener64/Bio3DView.jl
A Julia package to view macromolecular structures in the REPL, in a Jupyter notebook/JupyterLab or in Pluto
Language: Julia - Size: 10.8 MB - Last synced at: 2 days ago - Pushed at: 19 days ago - Stars: 36 - Forks: 7
tawssie/ZMPY3D
Python implementation of 3D Zernike moments with NumPy
Language: Python - Size: 15.4 MB - Last synced at: 14 days ago - Pushed at: 11 months ago - Stars: 11 - Forks: 2
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
Language: Jupyter Notebook - Size: 324 MB - Last synced at: 19 days ago - Pushed at: 5 months ago - Stars: 80 - Forks: 15
jvanheld/intro-bioinfo-L2-SV-AMU-SSV3U15_public
Cours d'introduciton à la bioinformatique, 2ème licence en Sciences de la vie, Aix-Marseille Université (L2 SV AMU)
Language: HTML - Size: 147 MB - Last synced at: 26 days ago - Pushed at: 26 days ago - Stars: 0 - Forks: 1
NoahHenrikKleinschmidt/buildamol
A fragment-based molecular assembly toolkit
Language: Python - Size: 183 MB - Last synced at: 20 days ago - Pushed at: about 1 month ago - Stars: 38 - Forks: 1
PDBeurope/protein-cluster-conformers
Clusters protein chains based on CA distance difference
Language: Python - Size: 105 MB - Last synced at: 13 days ago - Pushed at: 7 months ago - Stars: 15 - Forks: 0
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..
Language: Python - Size: 29.1 MB - Last synced at: 3 days ago - Pushed at: over 1 year ago - Stars: 80 - Forks: 16
drewschaub/protein-design-tools
A library of tools for protein design
Language: Python - Size: 1.97 MB - Last synced at: 17 days ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 0
Orpowell/alphafold-analyser
A tool to visualise the results of AlphaFold2 and inspect the quality of structural predictions
Language: Python - Size: 7.08 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 13 - Forks: 4
Electrostatics/pdb2cif
Convert between PDB and CIF formats
Language: Python - Size: 10.1 MB - Last synced at: 22 days ago - Pushed at: almost 4 years ago - Stars: 3 - Forks: 1
adenger/subpred_dl
Code for the manuscript "Application of Protein Structure Encodings and Sequence Embeddings for Transporter Substrate Prediction".
Language: Jupyter Notebook - Size: 21.4 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0
tawssie/ZMPY3D_PT
Python implementation of 3D Zernike moments with PyTorch
Language: Python - Size: 15.4 MB - Last synced at: 2 months ago - Pushed at: about 1 year ago - Stars: 4 - Forks: 0
ShravyaRS/Protein-structure-prediction-
Protein Structure Prediction Toolkit A Python-based tool to fetch, parse, and analyze protein 3D structures using PDB IDs. It downloads .pdb files from RCSB, extracts chain and residue information using BioPython, and sets the foundation for future integration with AlphaFold2 and structural analysis tools.
Language: Python - Size: 95.7 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0
tawssie/ZMPY3D_TF
Python implementation of 3D Zernike moments with Tensorflow
Language: Python - Size: 15.2 MB - Last synced at: 10 days ago - Pushed at: 11 months ago - Stars: 3 - Forks: 0
jgreener64/pdb-benchmarks
Benchmarking common tasks on proteins in various languages and packages
Language: Python - Size: 1.93 MB - Last synced at: 1 day ago - Pushed at: over 4 years ago - Stars: 42 - Forks: 7
SidSin0809/receptor-peptide-interface-mapper
High-throughput identification of receptor–peptide contact residues from PDB/mmCIF structures (Python 3, Biopython, multithreaded)
Language: Python - Size: 10.7 KB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0
Pranavkhade/PACKMAN
Python package built around protein structure and dynamics. OpenBabel-inspired objects.
Language: Python - Size: 12.3 MB - Last synced at: 7 days ago - Pushed at: 4 months ago - Stars: 36 - Forks: 7
samirelanduk/molstar-react
Molstar as a react component
Language: JavaScript - Size: 50.8 KB - Last synced at: 5 days ago - Pushed at: 5 months ago - Stars: 27 - Forks: 8
fraMade/MD_ligand_receptor
MD-ligand-receptor is a bioinformatics pipeline written in Python for analyzing non-covalent ligand-receptor interactions in 3D structures starting from a molecular dynamic trajectory.
Language: Python - Size: 25.3 MB - Last synced at: 3 months ago - Pushed at: about 2 years ago - Stars: 8 - Forks: 4
MooersLab/EasyPyMOL
Script to facilitate the making of horizontal scripts
Language: Python - Size: 646 KB - Last synced at: 4 months ago - Pushed at: over 1 year ago - Stars: 16 - Forks: 19
tawssie/ZMPY3D_CP
Python implementation of 3D Zernike moments with CuPy
Language: Python - Size: 15.2 MB - Last synced at: 16 days ago - Pushed at: 11 months ago - Stars: 3 - Forks: 0
johnnytam100/awesome-protein-design
A curated list of awesome protein design research, software and resources.
Size: 29.3 KB - Last synced at: 4 days ago - Pushed at: over 3 years ago - Stars: 14 - Forks: 1
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.
Language: Jupyter Notebook - Size: 6.61 MB - Last synced at: 2 months ago - Pushed at: 9 months ago - Stars: 1 - Forks: 0
jgreener64/ProteinEnsembles.jl
Generate and perturb protein structural ensembles using the ExProSE algorithm
Language: Julia - Size: 815 KB - Last synced at: 3 days ago - Pushed at: 11 months ago - Stars: 23 - Forks: 4
StrBio/strbio.github.io
StrBio 2023-24 @UAM
Language: TeX - Size: 84.9 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0
SerenaRosi/SerenaRosi
SerenaRosi's GitHub page
Size: 68.4 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 3 - Forks: 0
Sarah-Hesham-2022/Unity-Protein-Visualization
Protein Visualization using Unity and C# analysis on PDB Files.
Language: C# - Size: 229 KB - Last synced at: 5 months ago - Pushed at: over 2 years ago - Stars: 14 - Forks: 1
yamule/SurfStamp-public
3D Printer Compatible Molecular Surface Representation (Do not clone! Everything is in the release page!)
Size: 24.6 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 8 - Forks: 0
Electrostatics/go2pdb
Extract PDB entries annotated with specific GO codes
Language: Python - Size: 61.5 KB - Last synced at: 12 days ago - Pushed at: about 3 years ago - Stars: 2 - Forks: 3
bogrum/DockSpot
Ensemble docking tool project...
Language: Jupyter Notebook - Size: 722 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0
latticetower/chemprog-autumn2017
Course hometasks & additional links/materials on "Programming foundations for chemistry problems solving" - ITMO University, 2017 (some materials might be in Russian)
Language: HTML - Size: 8.5 MB - Last synced at: 9 months ago - Pushed at: over 7 years ago - Stars: 4 - Forks: 1
tikz/bio
Go library for parsing biological data formats and tool outputs from UniProt, PDB (Structure/Model/Chain/Residue/Atom - SMCRA), Pfam, DSSP, Fpocket and more. Plus: comparable position mappings!
Language: Go - Size: 193 KB - Last synced at: 7 days ago - Pushed at: about 3 years ago - Stars: 11 - Forks: 3
n-szulc/fingeRNAt
Software for detecting non-covalent interactions formed within complexes of nucleic acids with ligands.
Language: Python - Size: 14.4 MB - Last synced at: 5 months ago - Pushed at: over 3 years ago - Stars: 28 - Forks: 7
yamule/BF-align
Brute Force structural alignment
Language: Python - Size: 287 KB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0
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.
Language: C++ - Size: 8.48 MB - Last synced at: 3 months ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
cusbg/AHoJ-project
:wave: Webserver & command-line tool for search of APO (unbound) protein structures from HOLO (bound) forms and vice versa. http://apoholo.cz
Size: 5.7 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 5 - Forks: 1
DeepRank/PoNDeR
PointNet for Deep Rank: protein-protein interaction scoring using neural networks
Language: Python - Size: 383 KB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 9 - Forks: 1
gdocking/gdock
Protein-Protein Docking using Genetic Algorithm
Language: Python - Size: 6.65 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 14 - Forks: 2
Ahhmedsamehh/Bioinformatics_resources
This repo is dedicated to make bioinformatics resources available for anyone who wish to enter this field. (You may find it useful or not useful based on your level). I am still embarking my path in the field, just posting things based on my knowledge and the things which worked for me personally, they may/may not work with you, totally fine.
Size: 165 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 16 - Forks: 2
chaconlab/korpm
Predicting the effect of mutations on protein stability using a simple orientational potential.
Language: C++ - Size: 65.5 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 11 - Forks: 4
mitch-parker/rascore
A tool for analyzing RAS protein structures
Language: Python - Size: 296 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 36 - Forks: 34
csb-toolbox/CSB
A Python framework for structural bioinformatics.
Language: Python - Size: 5.45 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 12 - Forks: 3
RBVI/minrms
A bioinformatics algorithm for generating sequence alignments from 3D structures
Language: C++ - Size: 534 KB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 1
Sarah-Hesham-2022/BioPhysics-Molecular-Dynamics-Simulation
Using VMD and NAMD for molecular dynamics simulation of protein PDB files.
Language: Tcl - Size: 57.3 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 2
labstructbioinf/localpdb
Python package to manage protein structures and their annotations
Language: Python - Size: 1.72 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 38 - Forks: 4
magnitov/protease_annotation_pipeline
The code from the paper "An automated protocol for modelling peptide substrates to proteases"
Language: Python - Size: 479 KB - Last synced at: almost 2 years ago - Pushed at: about 4 years ago - Stars: 5 - Forks: 1
rsanchezgarc/BIPSPI
Partner specific prediction of protein binding sites
Language: Python - Size: 950 KB - Last synced at: 5 months ago - Pushed at: over 2 years ago - Stars: 8 - Forks: 9
haddocking/cyclic-peptides
Cyclic-peptide - protein complexes benchmark and associated scripts and data
Language: Shell - Size: 9.99 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 5 - Forks: 2
NikolasGialitsis/ProteinsDistanceGeometry
Exercises for MSc course "Algorithms in Structural Bioinformatics"
Language: Jupyter Notebook - Size: 958 KB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0
marcouderzo/StructuralBioinformatics-ContactNet Fork of TannerAGraves/StructBioInfo
Classification of Residue-Residue Interactions in Protein Structures using Deep Learning
Language: Python - Size: 36.7 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0
Andre-lab/ZEAL_commandLine
Command-line interface for ZEAL
Language: MATLAB - Size: 48 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 1
hackathonismb/VizSNP-St
Visualizing the effect of SNPs on protein structure using iCn3D
Language: Python - Size: 1.72 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 5 - Forks: 3
drippypale/structural-bio-project
This project consists of multiple tcl modules, which perform a few tasks on a given protein pdb file (NMR structure)
Language: Jupyter Notebook - Size: 555 KB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0
babaid/ProBindNN
My bachelors thesis on predicting relative protein-protein binding affinity changes upon point mutations using graph neural networks.
Language: Python - Size: 129 MB - Last synced at: 3 months ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0
Sarah-Hesham-2022/TCL-TK-VMD-PDB
TCL-TK for VMD.
Language: Tcl - Size: 230 KB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 0
jewettaij/dlpdb
collect statistics from the entire PDB library
Language: Python - Size: 2.02 MB - Last synced at: 1 day ago - Pushed at: over 3 years ago - Stars: 5 - Forks: 3
tikz/glycodist
3D distance from N-glycosylation sites to other residues, for all published glycoproteins. Evidence for the UGGT constraint we propose as the Parodi Limit. https://www.cell.com/structure/fulltext/S0969-2126(20)30464-0 https://en.wikipedia.org/wiki/UGGT
Language: Go - Size: 8.6 MB - Last synced at: 7 days ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0
tikz/VarMed
Web tool for the structural and functional analysis of human protein variants. https://varmed.qb.fcen.uba.ar
Language: JavaScript - Size: 64.5 MB - Last synced at: 7 days ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 1
MPBDS2022/Data-Science
Data Science Portfolio
Language: Jupyter Notebook - Size: 122 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0
davidmakoto/SuperBihelix-GPU-public
Boilerplate app for enabling parallel execution of pattented structural bioinformatics algorithm on GPUs using PyCUDA/CUDA framework.
Language: Python - Size: 66.4 KB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0
neksa/interactome
Structural Interactome pipeline
Language: JavaScript - Size: 68.2 MB - Last synced at: over 2 years ago - Pushed at: almost 6 years ago - Stars: 1 - Forks: 0
davidmakoto/pandos
Open source structural bioinformatics tool that enables novel analysis of G protein coupled receptor's (GPCR) domains.
Language: C# - Size: 82.7 MB - Last synced at: over 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0
jewettaij/minrms Fork of RBVI/minrms
A bioinformatics algorithm for generating sequence alignments from 3D structures
Language: C++ - Size: 530 KB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0
elifdogandar/StructuralBioinformatics-Phyton
Phyton codes for Structural Bioinformatics Questions
Language: Python - Size: 1.25 MB - Last synced at: over 2 years ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0
prcurran/pdb_superimposer
A small demo package for automated structural superimposition
Language: Python - Size: 5.96 MB - Last synced at: over 2 years ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0
gmagannaDevelop/Dimeres-Tetrameres
Projet Final cours BioInformatique Structurale II
Language: Python - Size: 1.07 MB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0
gmagannaDevelop/Structurale
Cours BioInformatique Structurale II : analyse via Python
Language: Jupyter Notebook - Size: 604 KB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 1
yamule/rust_pdbloader
A bunch of Rust snippet to play with data in PDB (https://www.rcsb.org/).
Language: Rust - Size: 11.1 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
AMarinhoSN/lPDBmngr
local PDB manager
Language: Python - Size: 20.5 KB - Last synced at: over 2 years ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0
GoodBoy962/StructuralBioinformatics
Final reports for structural bioinformatics classes with PyMOL
Language: HTML - Size: 101 MB - Last synced at: over 2 years ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0
TanguyLallemand/parse_dssp_output
(M2-Project) Construction a data set of protein structures gathering structures filtered
Language: Shell - Size: 1.39 MB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0
ravila4/RIVEM-chimera-plugin
RIVEM software plugin for UCSF Chimera
Language: Python - Size: 23.1 MB - Last synced at: over 2 years ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0
