Discover haddocking/cport Open Source project

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Python
License
Apache License 2.0
Created about 4 years ago
Updated about 2 months ago

haddocking

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

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haddock3

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haddock-tools

Set of useful HADDOCK utility scripts

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arctic3d

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

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fcc

Fraction of Common Contacts Clustering Algorithm for Protein Structures

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HADDOCK-antibody-antigen

Material to run the HADDOCK antibody-antigen modelling protocol

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powerfit

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

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prodigy-lig

Prediction of Protein-Small molecule binding affinities

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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

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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

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

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

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/cport

haddocking

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