structural-bioinformatics

There are 17 repositories under structural-bioinformatics topic.

biojava / biojava
:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
bioinformatics java protein-structure genomics protein-sequences protein-modification sequence-alignment structure-alignment protein-data-bank pdb parser-library structural-bioinformatics
Language:Java 585
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
JuliaMolSim / Molly.jl
Molecular simulation in Julia
molecular-dynamics julia protein-structure physics-simulation structural-bioinformatics molecular-simulation lennard-jones
Language:Julia 376
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
p2rank
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.
bioinformatics machine-learning protein-structure pdb binding-sites proteins ligand protein-surface structural-bioinformatics protein-ligand-interactions java random-forest mmcif pymol groovy protein-ligand-docking molecular-structures drug-discovery virtual-screening p2rank
Language:Groovy 234
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
diegozea / MIToS.jl
MIToS is 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
Language:Julia 72
harryjubb / arpeggio
Calculation of interatomic interactions in molecular structures
atomic-interactions bioinformatics cheminformatics structural-bioinformatics
Language:Python 66
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
Language:Python 65
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
jgreener64 / pdb-benchmarks
Benchmarking common tasks on proteins in various languages and packages
benchmarks bioinformatics comparison mmcif mmtf pdb pdb-files structural-bioinformatics
Language:Python 40
rascore
mitch-parker / rascore
A tool for analyzing RAS protein structures
structural-bioinformatics
Language:Python 40
labstructbioinf / localpdb
Python package to manage protein structures and their annotations
bioinformatics-tool bioinformatics-databases structural-bioinformatics
Language:Python 39
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
fingeRNAt
n-szulc / fingeRNAt
Software for detecting non-covalent interactions formed within complexes of nucleic acids with ligands.
nucleic-acids bioinformatics-tool structural-bioinformatics rna-ligand-complexes ligand-receptor-interaction drug-target-interactions ligand-target bioinformatics scientific-computing ligand-complex structural-interaction-fingerprint rna dna interactions molecular-interactions
Language:Python 27
samirelanduk / molstar-react
Molstar as a react component
molstar pdb protein-visualization bioinformatics structural-bioinformatics react
Language:JavaScript 24
jgreener64 / ProteinEnsembles.jl
Generate and perturb protein structural ensembles using the ExProSE algorithm
allosteric-predictions allostery coarse-grained julia paper protein-structure structural-bioinformatics
Language:Julia 22
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.
bioinformatics biotechnology machine-learning structural-bioinformatics structural-biology
19
chaconlab / korpm
Predicting the effect of mutations on protein stability using a simple orientational potential.
mutations protein-stability protein-structure structural-bioinformatics
Language:C++ 15
MooersLab / EasyPyMOL
Script to facilitate the making of horizontal scripts
pymol pml horizontal-scripts molecular-graphics molecular-visuallization protein-structure molecular-artwork pymol-macro-language molecular-structures biomolecular-structures structural-bioinformatics ambient-occulsion black-and-white-cartoons coordinate-covalent-bonds rna-structure metal-coordination scripting tutorial-videos startup-aliases roundview
Language:Python 15
gdocking / gdock
Protein-Protein Docking using Genetic Algorithm
protein-docking docking bioinformatics structural-biology computational-biology protein protein-structure protein-protein-interaction structural-bioinformatics genetic-algorithm chemistry rust
Language:Python 14
haddocking / haddocking.github.io
Webpage of the Bonvinlab @ Utrecht University and HADDOCK software
utrecht-university research education software integrative-modeling modeling protein-protein-interaction structural-bioinformatics structural-biology
Language:HTML 13
csb-toolbox / CSB
A Python framework for structural bioinformatics.
bioinformatics algorithms structural-bioinformatics library
Language:Python 12
johnnytam100 / awesome-protein-design
A curated list of awesome protein design research, software and resources.
alphafold alphafold-multimer alphafold2 bioinformatics bioinformatics-tool molecular-biology protein-design protein-function protein-sequence protein-structure structural-bioinformatics structural-biology protein-engineering protein-folding protein-protein-interaction protein-structure-prediction
11
Orpowell / alphafold-analyser
A tool to visualise the results of AlphaFold2 and inspect the quality of structural predictions
alphafold2 structural-biology structural-bioinformatics alphafold
Language:Python 10
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
Language:C# 10
DeepRank / PoNDeR
PointNet for Deep Rank: protein-protein interaction scoring using neural networks
deep-learning pdb point-cloud pointnet protein-protein-interaction structural-bioinformatics
Language:Python 9
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!
bioinformatics structural-bioinformatics
Language:Go 9
rsanchezgarc / BIPSPI
Partner specific prediction of protein binding sites
bioinformatics machine-learning protein-protein-interaction proteins structural-bioinformatics
Language:Python 8
yamule / SurfStamp-public
3D Printer Compatible Molecular Surface Representation (Do not clone! Everything is in the release page!)
bioinformatics protein-structure pdb structural-biology structural-bioinformatics biology 3dprinting visualization
7
AHoJ-project
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
bioinformatics alignment python pymol molstar structural-bioinformatics pdb mmcif rest-api webapp apo-holo fastapi protein-structure proteins protein-data-bank structural-biology protein-ligand-complex computational-biology drug-discovery
6
hackathonismb / VizSNP-St
Visualizing the effect of SNPs on protein structure using iCn3D
bioinformatics interactions mutation ngs protein-structure snps vcf visualization structural-bioinformatics
Language:Python 6
haddocking / cyclic-peptides
Cyclic-peptide - protein complexes benchmark and associated scripts and data
bioinformatics cyclic-peptides docking modelling proteins structural-bioinformatics utrecht-university
Language:Shell 6
magnitov / protease_annotation_pipeline
The code from the paper "An automated protocol for modelling peptide substrates to proteases"
structural-bioinformatics enzyme annotations
Language:Python 6
Sarah-Hesham-2022 / BioPhysics-Molecular-Dynamics-Simulation
Using VMD and NAMD for molecular dynamics simulation of protein PDB files.
bioinformatics biophysics molecular-dynamics-simulation namd pdb-files problem-solving programming proteins structural-bioinformatics structural-biology tcl-tk trajectory visulaization vmd nanoscale-molecular-dynamics visualization-molecular-dynamics force-filed waterbox
Language:Tcl 5

structural-bioinformatics

biojava / biojava

haddocking / pdb-tools

JuliaMolSim / Molly.jl

lightdock / lightdock

rdk / p2rank

BioJulia / BioStructures.jl

diegozea / MIToS.jl

harryjubb / arpeggio

MooersLab / pymolshortcuts

carlocamilloni / Structural-Bioinformatics

jgreener64 / pdb-benchmarks

mitch-parker / rascore

labstructbioinf / localpdb

jgreener64 / Bio3DView.jl

Pranavkhade / PACKMAN

n-szulc / fingeRNAt

samirelanduk / molstar-react

jgreener64 / ProteinEnsembles.jl

Ahhmedsamehh / Bioinformatics_resources

chaconlab / korpm

MooersLab / EasyPyMOL

gdocking / gdock

haddocking / haddocking.github.io

csb-toolbox / CSB

johnnytam100 / awesome-protein-design

Orpowell / alphafold-analyser

Sarah-Hesham-2022 / Unity-Protein-Visualization

DeepRank / PoNDeR

tikz / bio

rsanchezgarc / BIPSPI

yamule / SurfStamp-public

cusbg / AHoJ-project

hackathonismb / VizSNP-St

haddocking / cyclic-peptides

magnitov / protease_annotation_pipeline

Sarah-Hesham-2022 / BioPhysics-Molecular-Dynamics-Simulation