シュレーディンガー Official site

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.

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.

Integrated software for diverse biologics and antibody drug discovery, including monoclonal antibodies, vaccine antigens, enzymes, and peptides.

BioLuminate Our protein structure modeling technology allows for: 1. Prediction of structures of similar proteins, 2. Protein engineering functions such as a. aggregation prediction, b. hotspot identification, c. residue analysis, 3. Antibody modeling functions including a. CDR prediction from amino acid sequences, b. loop prediction, c. humanization, d. antigen-antibody docking simulation, 4. Protein-protein interaction analysis functions such as a. docking analysis, b. prediction of affinity changes due to residue mutations, c. alanine scanning, and other features. Protein FEP+ The energy analysis technology primarily based on free energy perturbation methods enables the calculation of high-precision predictions when applied to protein residues. Furthermore, by combining it with our BioLuminate, it allows for a comprehensive tool for a wide range of simulations in biology. #Biology #Modeling #Simulation #Prediction #Structure #Antibody #SmallMolecule #DrugDiscovery