What file types are supported for the light chain and heavy chain sequences required for antibody modeling?
Protean 3D supports the following protein file formats: .aa, .fap, .fas, .fasta, .gp, .gbk, .sbd, .pro.
What is the prediction method used for antibody modeling by 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.
How do I visualize the predicted antibody models?
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.
What details are available for each antibody model?
Available statistics for each antibody model include biophysical properties, structural properties, as well as details for each annotated hypervariable loop region. Results of the completed NovaFold Antibody prediction are also shown in a specialized report summarizing the identified loops and the template structures used for modeling.
Can I export an antibody structure model for publication?
Yes. Protean 3D lets you export the antibody structure itself or an image of the structure. To export the predicted antibody structure as a .pdb or .cif file, use File>Export Data > Export Structure. To export an image of the predicted antibody model in .png, .jpg or .gif format, use File > Export Image > Structure.
How can I model antibody-antigen interactions?
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.
