ANTIBODY MODELING

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 an antibody modeling prediction in NovaFold Antibody, the resulting .antibody structure file can be viewed and analyzed in Protean 3D, part of Lasergene Protein.  Protean 3D provides a graphical view of the structures, which allows you to visualize annotated features, including the six annotated CDR loops for light and heavy chains.

You can use NovaDock, part of Lasergene Protein, to predict the structure of antibody-antigen complexes by inputting the antibody and antigen structures. Simply provide your ligand and receptor PDB or structure files within NovaDock, 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.