Due to its complex nature, accurately modeling a protein-protein docking interaction can often prove to be very challenging. NovaDock molecular docking software offers the ability to predict protein-protein docking interactions for any two binding partners utilizing SwarmDock, one of the top algorithms validated in the CAPRI blind docking experiment. Utilizing the SwarmDock algorithm, NovaDock explores protein flexibility when docking, resulting in more accurate predictions. Simply provide your ligand and receptor PDB or structure files, proposing specific residue contacts between the binding partners if desired. NovaDock will then predict the three-dimensional structure of the macromolecular complex and provide energy score, cluster size, and number of ligand contacts for each model for analysis in Protean 3D.
Please see our resources below for more information on NovaDock molecular docking software.
Quality models and useful insights
“Using the suite of DNASTAR programs, NovaFold, NovaFold Antibody, and NovaDock, I have generated functional models of antibody-antigen complexes from the component’s amino acid sequences. The quality of the models and the useful insights they generate more than justify the effort and computing time.”
Do you offer a free trial of NovaDock?
One prediction for each of our Nova Applications is included in our Lasergene free trial. We also offer free, no-obligation, personalized demos of any of our Nova Applications with one of our scientists on staff, tailored to your specific research objectives.
What is the protein-protein docking prediction method used?
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. 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.”
Can I use NovaDock to model antibody-antigen interactions?
You can use NovaDock to predict the structure of antibody-antigen complexes by inputting the antibody and antigen structures. If you don’t have an experimental antibody structure, first model the structure using NovaFold Antibody, which is specifically designed to generate models of antibodies and antibody fragments (Fv, Fab, VH, sdAb) starting from sequence data. The NovaFold Antibody algorithm utilizes a combination of homology modeling and ab initio loop prediction, resulting in highly accurate predictions which can then be used in NovaDock.