NovaFold Antibody is specifically designed to generate models of antibodies and antibody fragments (Fv, Fab, VH, sdAb) and, with the use of NovaDock, predict the structure of antibody-antigen complexes. DNASTAR provides NovaFold Antibody as a local or cloud-based, separately licensed service within Protean 3D™. Antibodies frequently have two chains of interest: a light and a heavy chain. When you submit a prediction using NovaFold Antibody, you can provide a light chain, a heavy chain, or both. If you submit two chains, the software will model the complex; if you submit one, it will instead model the chain.

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

The following video is a brief introduction to NovaFold Antibody:

The NovaFold Antibody algorithm utilizes a combination of homology modeling and ab initio loop prediction, resulting in highly accurate predictions. During modeling, NovaFold Antibody searches the input sequence(s) against thousands of non-redundant protein antibody structures from PDB and finds the best template matches for the chain or complex.

During modeling, NovaFold Antibody gives particular consideration to the complementary determining region (CDR) loops, hypervariable regions of an antibody that react dominantly with an antigen. The three CDR loops on the heavy chain are known as H1, H2 and H3, while the three on the light chain are L1, L2 and L3. H3 is commonly the most important region in antigen binding. Due to its increased length and flexibility, it is also the most difficult to model. As such, NovaFold Antibody limits H3 loop modeling to fifteen or fewer residues, a length commonly seen in antibody modeling problems. Finally, NovaFold Antibody performs energy minimization calculations to construct the final predicted structure model for the antibody chain or complex. This entire process takes approximately 5-15 minutes on a standard workstation computer.

After running a NovaFold Antibody prediction, the resulting .antibody structure file can be viewed and analyzed in DNASTAR’s Protean 3D application. Protean 3D’s Structure view and Features panel facilitate examination of antibody features, including the six annotated CDR loops for light and heavy chains.

NovaFold Antibody can also be used to create an input structure for NovaDock, DNASTAR’s protein-protein docking application that can also be used to predict atomic-level antibody/antigen interactions. When setting up a NovaDock prediction, simply use Protean 3D to export the predicted structure in PDB format and specify the exported file as one of the two binding partners.

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