structural-biology

There are 17 repositories under structural-biology topic.

graphein
a-r-j / graphein
Protein Graph Library
bioinformatics computational-biology deep-learning dgl drug-discovery gene-regulatory-networks geometric-deep-learning graph-neural-networks interactome interactomics ppi-networks protein protein-data-bank protein-design protein-structure python pytorch pytorch-geometric rna structural-biology
Language:Jupyter Notebook 1003
MolecularNodes
BradyAJohnston / MolecularNodes
Toolbox for molecular animations in Blender, powered by Geometry Nodes.
blender biochemistry geometry-nodes protein protein-structure protein-visualization sciart visualisation structural-biology blender-addon protein-data-bank molecule proteins pdb molecular-modeling
Language:Python 850
biotite
biotite-dev / biotite
A comprehensive library for computational molecular biology
bioinformatics computational-biology structural-biology sequence-analysis pdb-files
Language:Python 583
haddocking / pdb-tools
A dependency-free cross-platform swiss army knife for PDB files.
python protein pdb bioinformatics structural-biology structural-bioinformatics rcsb utrecht-university
Language:Python 378
jonathanking / sidechainnet
An all-atom protein structure dataset for machine learning.
dataset deep-learning machine-learning protein-structure structural-biology
Language:Python 323
lightdock
lightdock / lightdock
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
protein protein-structure protein-protein-interaction protein-docking swarm-intelligence glowworm-swarm-optimization protein-dna-interactions peptides dna docking artificial-intelligence protein-design proteomics structural-biology structural-bioinformatics bioinformatics bioinformatics-tool chemistry molecular-biology molecular-structures
Language:Python 297
project-gemmi / gemmi
macromolecular crystallography library and utilities
cif mmcif crystallography protein-structure molecular-structures ccp4 pdb-files structural-biology mtz
Language:C++ 206
Genentech / equifold
Official code repository for EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation
machine-learning structure-prediction proteins structural-biology
Language:Python 116
jonathanking / protein-transformer
Predicting protein structure through sequence modeling
protein-structure sequence-to-sequence attention computational-biology machine-learning structural-biology
Language:Jupyter Notebook 106
mittinatten / freesasa
C-library for calculating Solvent Accessible Surface Areas
c bioinformatics structural-biology pdb
Language:C 103
samirelanduk / atomium
Python macromolecular parsing (with .pdb/.cif/.mmtf parsing and production)
biology proteins structural-biology chemistry molecules
Language:Python 102
SBRG / ssbio
A Python framework for structural systems biology
cobrapy constraint-based-modeling protein-structure structural-biology structural-systems-biology systems-biology
Language:Python 102
molstar / VSCoding-Sequence
VSCode Extension for interactively visualising protein structure data in the editor
vscode vscode-extension protein protein-structure pdb pdb-files molstar molecule structural-biology structure
Language:TypeScript 95
BioJulia / BioStructures.jl
A Julia package to read, write and manipulate macromolecular structures
bioinformatics structural-biology julia pdb protein-structure biology structural-bioinformatics biojulia
Language:Julia 92
phonchi / Computational-CryoEM
A curated list of awesome computational cryo-EM methods.
cryo-em electron-microscopy single-particle-analisys computational-biology structural-biology cryoem
Language:Jupyter Notebook 86
pensa
drorlab / pensa
PENSA - a collection of python methods for exploratory analysis and comparison of biomolecular conformational ensembles.
biomolecules biophysics molecular-dynamics structural-biology
Language:Python 80
I2PC / scipion
Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM)
electron-microscopy cryo-em single-particle-analisys structural-biology workflow reproducible-science usability image-processing python c-plus-plus
Language:Python 76
BALL-Project / ball
The Biochemical Algorithms Library
c-plus-plus structural-biology chemoinformatics force-field computational-biology drug-design
Language:C++ 72
salilab / imp
The Integrative Modeling Platform
protein-structure python c-plus-plus structural-biology integrative-modeling
Language:C++ 70
proteinevolution / Toolkit
The MPI Bioinformatics Toolkit
bioinformatics protein-structure web-application reactive-programming structural-biology computational-biology sequence-search profile-search open-source profile-profile-search akka play-framework typelevel
Language:Scala 62
cxhernandez / ipymol
Control PyMOL sessions via IPython
python visualization structural-biology notebook
Language:Python 55
cbalbin-bio / pymol-color-alphafold
PyMOL extension to color AlphaFold structures by confidence (pLDDT).
alphafold alphafold2 bioinformatics computational-biology protein-structure structural-biology pymol pymol-plugin
Language:Python 54
chopralab / lemon
A framework for rapidly mining structural information from the Protein Data Bank
structural-biology computational-chemistry cheminformatics chemistry data-mining machine-learning
Language:C++ 52
proteinsolver
ostrokach / proteinsolver
Graph neural network for generating novel amino acid sequences that fold into proteins with predetermined topologies.
protein-sequence protein-structure protein-design graph-neural-networks protein bioinformatics structural-biology
Language:Jupyter Notebook 51
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
molecular-dynamics structural-bioinformatics structural-biology teaching-materials
Language:Jupyter Notebook 45
haddocking / haddock-tools
Set of useful HADDOCK utility scripts
computational-structural-biology haddock integrative-modeling python structural-biology utrecht-university
Language:Python 45
lbcb-sci / RiNALMo
RiboNucleic Acid (RNA) Language Model
bioinformatics biology foundation-model language-model rna rna-secondary-structure rna-seq rna-structure-prediction secondary-structure splice-site-prediction structural-biology
Language:Python 45
freesasa / freesasa-python
FreeSASA Python Module
python pypi-packages structural-biology
Language:Cython 43
jgreener64 / Bio3DView.jl
A Julia package to view macromolecular structures in the REPL, in a Jupyter notebook/JupyterLab or in Pluto
protein-structure structural-bioinformatics jupyter-notebook structural-biology julia bioinformatics ijulia pluto
Language:Julia 33
PACKMAN
Pranavkhade / PACKMAN
PACKMAN: PACKing and Motion ANalysis
protein alpha-shape protein-structure protein-hinge-prediction pdb-parser protein-domain-identification structural-bioinformatics structural-biology python
Language:Python 32
DeepRank / deeprank2
An open-source deep learning framework for data mining of protein-protein interfaces or single-residue variants.
convolutional-neural-networks deep-learning graph-neural-networks protein-protein-interfaces pytorch single-residue-variants structural-biology
Language:Python 31
mdciao
gph82 / mdciao
mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data
molecular-dynamics computational-chemistry structural-biology python pdb-database amino-acids protein-structure gpcr gpcr-numbering kinases
Language:Python 30
ZauggGroup / DeePiCt
Pipeline for the automatic detection and segmentation of particles and cellular structures in 3D Cryo-ET data, based on deep learning (convolutional neural networks).
deep-learning biology structural-biology cnn segmentation unet cryo-et
Language:Python 28
TomoBEAR
KudryashevLab / TomoBEAR
TomoBEAR is a configurable and customizable modular pipeline for streamlined processing of cryo-electron tomographic data for subtomogram averaging.
cryo-em cryoem cryo-et cryoet processing pipeline structural-biology parallel cluster-computing parallel-computing cluster tem em et tomography reconstruction automated alignment particle-picking template-matching
Language:MATLAB 26
phonchi / Computational-CryoET
A curated list of awesome computational cryo-ET methods.
computational-biology cryo-et cryoet electron-microscopy structural-biology
26
MPI-Dortmund / pymissense
PyMissense creates the pathogenicity plot and modified pdb as shown in the AlphaMissense paper for custom proteins.
deep-learning protein-sequences protein-structure protein-structure-prediction uniprot structural-biology
Language:Python 20