Discover haddocking/SARS-COV2-NTD-SIA-modelling Open Source project

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Apache License 2.0
Created about 4 years ago
Updated almost 4 years ago

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Modelling of the binding of various sialic acid-containing oligosaccharides to the NTD domain of the spike protein of SARS-CoV2

pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.

Python

388

prodigy

Predict the binding affinity of protein-protein complexes from structural data

Python

110

haddock3

Official repo of the modular BioExcel version of HADDOCK

Python

103

haddock-tools

Set of useful HADDOCK utility scripts

Python

arctic3d

Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information

Python

fcc

Fraction of Common Contacts Clustering Algorithm for Protein Structures

Python

HADDOCK-antibody-antigen

Material to run the HADDOCK antibody-antigen modelling protocol

Python

powerfit

Rigid body fitting of atomic strucures in cryo-electron microscopy density maps

Python

prodigy-lig

Prediction of Protein-Small molecule binding affinities

Python

haddocking.github.io

Webpage of the Bonvinlab @ Utrecht University and HADDOCK software

HTML

binding-affinity-benchmark

Protein-protein binding affinity benchmark

BM5-clean

Docking benchmark 5 - cleaned and ready to use for HADDOCK

Roff

protein-peptide-docking_1CZY

Python

disvis

Visualisation of conformational space restriction by distance restraints

Python

prodigy-cryst

Contacts-based classifier of biological and crystallographic interfaces

Python

MemCplxDB

Membrane protein complexes docking benchmark

cyclic-peptides

Cyclic-peptide - protein complexes benchmark and associated scripts and data

Shell

3D-DART-server

3D-DART web server repository

Python

iSee

DACUM

The Database of binding Affinity Change Upon Mutations in protein complexes

HADDOCK-binding-sites-tutorial

Shell

Prot-DNABenchmark

Protein-DNA docking benchmark

EDES

Shell

shape-restrained-haddocking

Python

ai-antibodies

Jupyter Notebook

3D-DART

Standalone code for 3D-DART (originally developed by Marc van Dijk)

Python

protein-glycans

Python

whiscy

Bioinformatic tool to predict structural protein-protein interfaces

haddock-mmcif

Encode information from a HADDOCK run to a cif file to be deposited in PDB-Dev.

Python

haddock-runner

Run large scale HADDOCK simulations using multiple input molecules in different scenarios

cport

CPORT is a Consensus Prediction Of interface Residues in Transient complexes used to predict protein-protein interface residues.

Python

CASP-CAPRI-T70-tutorial

Shell

powerfit-tutorial

Simple tutorial to showcase the use of PowerFit.

Shell

D3R-tools

A collection of scripts of data relating to the D3R Grand Challenge competitons

MATLAB

haddock_param_tools

Python scripts to manipulate HADDOCK2.4 parameter files (*.json)

Python

fandas

Repository of the FANDAS code for prediction ssNMR spectra from structure

Python

samplex

Python

MD-scoring

Script and associated data for MD-based scoring of HADDOCK clusters

Jupyter Notebook

protein-peptide

Protein-peptide HADDOCK-ready docking benchmark

contact-filtering

DisVis-based filtering of contacts from co-evolution data (or other sources)

Shell

physiological_homodimers_benchmark

Python

vmbuilder

VM Appliance Developer Environment

Shell

refine-EM-complexes

Repository containing the data set, analysis results and scripts associated with our manuscript on "Interface Refinement of Low-to-Medium Resolution Cryo-EM Complexes using HADDOCK2.4"

Jupyter Notebook

proABC-2

Deep learning framework to predict antibody paratope residues

Python

haddock24-protocol

Data for performing HADDOCK2.4 protocols

haddock-restraints

Generate restraints to be used in HADDOCK

Rust

haddocking/SARS-COV2-NTD-SIA-modelling

haddocking

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