OpenEye’s suite of antibody modeling tools, accessed via the cloud platform Orion, includes Specifica’s state-of-the-art antibody sequence analysis tool AbXtract and open-source tools such as ImmuneBuilder for antibody structure prediction. In this webinar, Dr. Jesper Sørensen will guide viewers through the process of modeling antibody structure on Orion, which begins with taking sequences from a selection campaign analyzed using AbXtract, or other methods such as internal or public databases. 3D structures are then generated with the AI-driven structure predictor ImmuneBuilder (requiring only around 100 ms per structure when predicting at the multi-thousand scale). From these structures a wide variety of physico-chemical properties are calculated to enable selection of those antibodies/sequences most likely to be successfully developed into human therapies. Structural diversity in the complementarity-determining region (CDR) can be further explored using knowledge-based loop modeling, while molecular dynamics and enhanced sampling molecular dynamics is used to explore global conformational diversity. Structural families within computed ensembles can be identified by clustering using similarity based on a physically rigorous shape and chemical feature distribution of the CDRs. Individual sequences can be further optimized by single or multi-point mutations and/or loop replacement and these new hypotheses submitted to physico-chemical property profiling and conformational exploration.
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About the speaker:
Jesper Sørensen is the head of biomodeling at OpenEye, Cadence Molecular Sciences. He received his Ph.D. in Nanoscience (chemistry) from Aarhus University in Denmark and subsequently did a post-doc in Prof. Rommie Amaro’s lab at UC San Diego in California. From there he joined a biotech company, Dart Neurosciences, as a scientific software developer. In 2018 Jesper joined OpenEye Scientific Software, where he co-developed the Spruce toolkit for protein structure preparation. He now manages a developer team focused on making advancements in drug discovery tools for biologics.
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