Jon Kapla

Background

About Jon Kapla

Physical chemist with a particular interest in molecular interactions and molecular modeling. I'm currently working as a scientist at Cytiva, leveraging state of the art AI methods for protein and peptide binder design such as RFDiffusion, ProteinMPNN, ESM and Alphafold2. Previously, I have used my knowledge to aid the development of the next generation IgG cleaving enzymes at Hansa Biopharma. I used modeling and molecular visualization as tools to aid development and stabilization of proteins and to aid the understanding of how an IgG cleaving enzyme interacts with the target antibody. I also invented and evaluated exploratory ideas as well as investigated interesting assets through patents and available litterature. I have used my python skills to analyze models and simulations as well as to aid experimentalists with automatized workflows to analyze and visualize Elispot/Fluorospot data for immunogenicity assessments. I created a web application for bulk visualization of new candidate protein molecules with a clear view of incorporated amino acid changes for the team to be able to compare and discuss the candidates in more detail. I also designed molecular wall decorations for the company's new office space. I have used cloud computing resources to set up, use and analyze molecular dynamics simulations, homology modeling and AI models such as AlphaFold2 and Evolutionary Scale Modeling (ESM). As a proof of concept example, I managed to increase the melting point of an enzyme by several degrees utilizing ESM inverse folding and sequence scoring to guide stabilizing point mutations. In my Ph.D, I focused on the interplay between carbohydrate molecules and lipid bilayers. At Uppsala University I extended my views working with computer modeling of G-protein coupled receptors (GPCRs) to find new drug candidates. By using methods such as molecular dynamics simulations and molecular docking, I characterized homology models and how small molecules bind to the receptors. As a computational chemist, I am highly skilled in automatizing tasks and advanced Linux usage. Specialties: Physical chemistry, antibody modeling, IgG cleaving enzymes, G-protein coupled receptors, Lipid bilayers, Model membranes, Carbohydrates, Molecular dynamics simulations, Molecular visualization, Molecular docking, Molecular modeling, Protein design, RFDiffusion, Alphafold2, ESM, Linux, Bash, Python Publication list: