Collaborative Science

Accelerating time to market and driving innovation with collaboration, knowledge based understanding and prediction.

Antibody Modeling

Discovery Studio delivers the most complete solution for antibody design and optimization. Construct a modeling framework for antibodies, predict antibody physical properties and optimize both pH or thermal stability and formulation developability.

Antibody modeling capabilities include:

  • Automated modeling cascade to easily generate high quality 3D antibody full-length, bispecific, Fab or Fv models from a set of light and heavy antibody chain sequences
  • Simultaneously and independently perform multiple sequence alignments of heavy and light chains
  • Identify antibody template structures
  • Filter templates by canonical structures
  • Build high quality Homology models
  • Graft Fab models onto a full-length template
  • Use standard CDR loop definitions: IMGT, Chotia, Honegger, Kabat
  • Refine CDR loops using either template, loop grafting or ab initio loop modeling
  • Enhanced De Novo Loop prediction
  • Refine residue side chains
  • Perform detailed model analysis
  • Predict protein ionization and residue pKs
  • Protonate residues at a given pH, based on predicted pKs
  • Calculate the total protein charge as a function of pH
  • Predict the isoelectric point (pI)
  • Conduct Thermal or pH-based mutational stability predictions
  • Identify stable disulfide bridge locations
  • Perform antigen-antibody docking using ZDOCK
  • Identify critical interacting residues
  • Perform either implicit solvent-based or explicit solvent-based Molecular Dynamics (MD) simulations using CHARMm c42b1
  • Calculate Temperature- or pH-based mutational binding affinity prediction
  • Calculate aggregation propensity
  • Calculate the Developability Index of IgG1 antibodies
  • Predict residue mutations to make an antibody more human compatible without compromising antibody stability
  • Calculate mean atomic charges, average dipole moment, net charge, electrostatic contribution to the solvation energy as a function of pH
  • Predict sites prone to Post Translational Modifications (PTMs) using sequence-based motif searching

Read the Discovery Studio Antibody Modeling Datasheet

Read the application brief on “Antibody Structure Modeling with Discovery Studio”

Learn more about the comprehensive BIOVIA Biologics Solution for Discovery