NovaDock: protein-protein docking

NovaDock is a protein docking application that runs within the Protean 3D interface. DNASTAR provides NovaDock as a local or cloud-based, separately licensed service within Protean 3D. NovaDock’s algorithm is based on SwarmDock, developed in Dr. Paul Bates’ laboratory at the Cancer Research UK’s London Research Institute, and ongoing at the Francis Crick Institute. The SwarmDock algorithm is provided to DNASTAR under license from Cancer Research Technology Limited.

For step-by-step instructions, see Run NovaDock through Protean 3D, Run Nova applications through the DNASTAR website, or Run Nova applications locally.

The following video is a brief introduction to NovaDock:

NovaDock is used to predict atomic interactions between two binding partners, both of which must be proteins. One binding partner is the ligand (‘L’: usually the smaller partner or an antibody); the other is the receptor (‘R’: usually the larger partner or an antigen). Each binding partner can consist of one or multiple protein chains. NovaDock does not use a library of templates, but instead makes docking predictions based on a type of energy calculation known as “particle swarm optimization.”

One of several optional arguments directs NovaDock to use residues which are believed (or known) to be in the protein interface.

NovaDock requires a complete protein structure that uses only standard residues and has no missing residues, atoms or chains. Before the docking simulation, NovaDock automatically replaces any missing atoms or replaces non-standard residues with the closest natural equivalent. If any missing data were replaced, the NovaDock Report (viewed within Protean 3D), will include a notation to that effect in its Details panel. NovaDock then uses “normal modes of motion” to explore protein flexibility during the docking simulation.

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If you would like to cite NovaDock in a publication, please use the following:

“NovaDock (DNASTAR, Madison, WI)” or “DNASTAR’s NovaDock”

The following references describe the SwarmDock algorithm that is used in NovaDock:

• M. Torchala, I. H. Moal, R. A. G. Chaleil, J. Fernandez-Recio, P. A. Bates, ‘SwarmDock: a server for flexible protein-protein docking’, Bioinformatics 29, 807-809 (2013).
  
  
• M. Torchala, I. H. Moal, R. A. G. Chaleil, R. Agius, P. A. Bates, ‘A Markov-chain model description of binding funnels to enhance the ranking of docked solutions’, Proteins 81, 2143-2149 (2013).
  
  
• M. Torchala, P. A. Bates, ‘Predicting the Structure of Protein-Protein Complexes Using the SwarmDock Web Server’, in: Protein Structure Prediction 3rd Edition (Methods in Molecular Biology, Vol. 1137), Humana Press, 2014.