HADDOCK3

HADDOCKer

Docker image for the running the HADDOCK system for predicting the structure of biomolecular complexes.

Colby T. Ford, Ph.D. and Rafael Jaimes III, Ph.D.

Pull from DockerHub

If you don't want to build the image you can see a list of prebuilt versions on DockerHub here: https://hub.docker.com/r/cford38/haddock/tags

docker pull cford38/haddock:3

Build Instructions

1. Clone this repository to your local machine

2. Open terminal and navigate to the directory of this repository.

3. Run the following command. This will generate the Docker image.

docker build -t haddock3 .

4. Once the container is ready, remote into the bash terminal.

docker run --name haddock3 -it haddock3 /bin/bash
# docker exec -it haddock3 /bin/bash

Running in Singularity

If you'd like to use this Docker image in a high-performance computing environment that requires Singularity, simply pull and convert the image using the following logic:

## Load the Singularity module
module load singularity

## Pull the Docker image from DockerHub and output a .sif file
singularity pull haddock3.sif docker://cford38/haddock:3

## Run commands inside the container interactively
singularity run haddock3.sif /bin/bash

## or execute the HADDOCK3 application directly
singularity exec haddock3.sif haddock3 config.cfg

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Licensing

This container image includes software libraries that each require a license. Please fill out the following license request forms before using this software:

• HADDOCK 3: https://github.com/haddocking/haddock3
• CNSsolve 1.3: http://cns-online.org/v1.3/

Citations

HADDOCK:

• Cyril Dominguez, Rolf Boelens and Alexandre M.J.J. Bonvin. HADDOCK: a protein-protein docking approach based on biochemical and/or biophysical information. J. Am. Chem. Soc. 125, 1731-1737 (2003).
• G.C.P van Zundert, J.P.G.L.M. Rodrigues, M. Trellet, C. Schmitz, P.L. Kastritis, E. Karaca, A.S.J. Melquiond, M. van Dijk, S.J. de Vries and A.M.J.J. Bonvin. "The HADDOCK2.2 webserver: User-friendly integrative modeling of biomolecular complexes." J. Mol. Biol., 428, 720-725 (2016).

CNSsolve:

• A.T. Brunger, P.D. Adams, G.M. Clore, P.Gros, R.W. Grosse-Kunstleve, J.-S. Jiang, J. Kuszewski, N. Nilges, N.S. Pannu, R.J. Read, L.M. Rice, T. Simonson, G.L. Warren,Crystallography & NMR System (CNS), A new software suite for macromolecular structure determination, Acta Cryst.D54, 905-921(1998).
• A.T. Brunger, Version 1.2 of the Crystallography and NMR System, Nature Protocols 2, 2728-2733 (2007).