Challenging the structural prediction of unstructured epitopes and long CDR H3 loops.
Application of replica exchange MD to the structural prediction of antigen-antibody complexes with long CDR H3 loops and disordered epitopes exceeding several dozen residues.
Schrödinger's drug discovery platform utilizes computational chemistry techniques based on the first principles of physics, enabling advanced drug design based on protein structural information, and is being utilized by major pharmaceutical companies worldwide. We will present the latest results of antigen-antibody simulations using our software at the seminar below. 22nd Annual Meeting of the Japanese Society for Protein Science Luncheon Seminar [Date and Time] June 7 (Tuesday) 12:00 - 12:50 Venue: Tsukuba International Conference Center 2F E Hall Session ID: LS1E [Program] Schrödinger's approach to physics-based antibody analysis and design: dealing with disordered epitopes and very long CDR H3 loop We will also have a booth at the corporate exhibition, so please stop by. You can experience Schrödinger's Biologics Modeling Suite: BioLuminate.
basic information
In this seminar, we will explain the general 3D modeling techniques for antibodies using Schrödinger's Biologics Modeling Suite: BioLumimate, as well as the prediction of antigen-antibody complex structures using protein-protein docking and affinity and stability predictions using the Free Energy Perturbation (FEP) method. We will also discuss the potential for estimating the structure of antigen-antibody complexes using MD simulations and orthogonal experimental data for antigens with disordered epitopes that do not have specific stable conformations on their own. Furthermore, we have recently demonstrated that this method is highly effective for predicting the complex structures of antibodies and antigens with long CDR H3 loops exceeding 20 amino acid residues. In this seminar, we will present examples of predicting these very long H3 loop structures, including comparisons with predictions made by AlphaFold2.
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