Best Software and Webserver for Antibody Design

Antibody design is a process of creating new antibodies that can bind to specific targets, such as antigens, toxins, or drugs. Antibodies are proteins that play a vital role in the immune system, as they can recognize and neutralize foreign substances that cause diseases.

Antibody design can be used for various purposes, such as developing new therapeutics, diagnostics, or vaccines.

The antibody design process involves several steps and considerations, such as:

• Synthesize or purify the target antigen (e.g., peptide or hapten)
• Choose an appropriate immunogenic carrier protein
• Conjugate the antigen and carrier protein to create the immunogen
• Immunize an animal (e.g., mouse, rabbit, or goat) with the immunogen
• Collect the serum or isolate the B cells from the immunized animal
• Screen the serum or B cells for the presence of antibodies that bind to the antigen
• Purify the antibodies from the serum or B cells
• Characterize the antibodies for their specificity, affinity, and functionality
• Optimize the antibodies for their stability, solubility, and expression
• Humanize the antibodies if they are derived from non-human sources
• Modify the antibodies for their labeling, immobilization, or fragmentation

There are many software and webserver tools that can assist you with antibody design, depending on your needs and preferences. Some of them are:

• ProteinMPNN¹: This is a software tool developed by the Institute for Protein Design at the University of Washington. It can quickly identify new amino acid sequences that are likely to fold into a given protein backbone structure. It can also generate predicted antibody structures from the selected sequences, as well as evaluate their binding affinity to the target antigen.
• NovaFold Antibody²: This is a web server developed by DNASTAR. It uses a unique algorithm that combines homology modeling for framework regions and fragment-based or ab initio modeling for hypervariable loop regions, resulting in highly accurate antibody structure predictions. It can also be used in conjunction with NovaDock to predict the structure and binding of antibody-antigen complexes.
• Antigen Prediction Tool³: This is a web server developed by GenScript. It allows you to search your optimal peptide antigens from a database of over 100 million peptides generated by GenScript’s OptimumAntigen Design Program. Each peptide is optimized using the industry’s most advanced antigen design algorithm, which considers various criteria such as sequence length, hydrophilicity/hydrophobicity, surface orientation and flexibility, continuous vs. discontinuous epitopes, secondary structure regions, avoidance of specific sequence motifs, epitope analysis and coupling strategy.
• SAbPred: This is a collection of computational tools developed by the Oxford Protein Informatics Group (OPIG). It can perform various tasks related to antibody structure prediction and annotation, such as Fv modelling (ABodyBuilder-ML), antibody structure modelling (ABodyBuilder2), TCR structure modelling (TCRBuilder2), nanobody structure modelling (NanoBodyBuilder2), side chain prediction (PEARS), sequence numbering (ANARCI), canonical form prediction from sequence (SCALOP), developability prediction (TAP), antibody humanisation tool (Hu-mAb).

Tags: Antibody_Design, Antigen