haddocking/refine-EM-complexes

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haddocking/refine-EM-complexes

haddocking

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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"

pdb-tools

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

prodigy

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

haddock3

Official repo of the modular BioExcel version of HADDOCK

haddock-tools

Set of useful HADDOCK utility scripts

arctic3d

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

fcc

Fraction of Common Contacts Clustering Algorithm for Protein Structures

HADDOCK-antibody-antigen

Material to run the HADDOCK antibody-antigen modelling protocol

powerfit

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

prodigy-lig

Prediction of Protein-Small molecule binding affinities

haddocking.github.io

Webpage of the Bonvinlab @ Utrecht University and HADDOCK software

binding-affinity-benchmark

Protein-protein binding affinity benchmark

BM5-clean

Docking benchmark 5 - cleaned and ready to use for HADDOCK

protein-peptide-docking_1CZY

disvis

Visualisation of conformational space restriction by distance restraints

prodigy-cryst

Contacts-based classifier of biological and crystallographic interfaces

MemCplxDB

Membrane protein complexes docking benchmark

cyclic-peptides

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

3D-DART-server

3D-DART web server repository

iSee

DACUM

The Database of binding Affinity Change Upon Mutations in protein complexes

HADDOCK-binding-sites-tutorial

Prot-DNABenchmark

Protein-DNA docking benchmark

EDES

shape-restrained-haddocking

ai-antibodies

Jupyter Notebook

3D-DART

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

protein-glycans

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.

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.

CASP-CAPRI-T70-tutorial

powerfit-tutorial

Simple tutorial to showcase the use of PowerFit.

D3R-tools

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

haddock_param_tools

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

fandas

Repository of the FANDAS code for prediction ssNMR spectra from structure

samplex

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)

physiological_homodimers_benchmark

vmbuilder

VM Appliance Developer Environment

SARS-COV2-NTD-SIA-modelling

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

proABC-2

Deep learning framework to predict antibody paratope residues

haddock24-protocol

Data for performing HADDOCK2.4 protocols

haddock-restraints

Generate restraints to be used in HADDOCK