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HADDOCK2.4

README.md

HADDOCKer

Docker image for the running the HADDOCK system v2.4 for predicting the quarternary structure of biomolecular complexes.

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

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.
    This builds for 24 cores by default.

docker build -t haddock2_4 .

Optionally, you may override the number of cores used. For example, to build for 64 cores, set the CORES build argument to 64.

docker build -t haddock2_4 . --build-arg CORES=64
  1. Once the container is ready, remote into the tcsh terminal.
# docker run --name haddock2_4 -d haddock2_4
## Mount a volume on your local machine
docker run -v T:\haddock_tests:/data --name haddock2_4 -d haddock2_4
docker exec -it haddock2_4 /bin/tcsh

Usage

cd $HOME/haddock/haddock2.4-2021-01/
# source haddock_configure.csh

cd examples/protein-protein

# haddock2.4 run.cns
# cd run1
# haddock2.4 run.param

./run-example.csh

## Find the best PDB based on HADDOCK Score
cluster_haddock-score.txt_best4
file.nam_clust1_haddock-score
nano protein-protein_3.pdb

Notes

  • The ana_scripts/ folder is very useful for performing the post analysis on the HADDOCK run.

Licensing

This container image includes software libraries that each require a license (and may limit use to non-profit/academic work). Please fill out the following license request forms before using this software:

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).

Push to Container Registry

docker tag haddock2_4 <USERNAME>/haddock:2.4
docker push <USERNAME>/haddock:2.4

# docker tag haddock2_4 cford38/haddock:2.4
# docker push cford38/haddock:2.4