Research

Facilitating Search in the High-Dimensional Space of Molecular Interactions

The binding of proteins (receptors) to small molecules (ligands) is often the underlying mechanism behind biological processes such as immune response and cell signaling. Understanding how receptors and ligands bind is fundamental to explaining these biological phenomena, and for innovative drug discovery and design. In this work we design methods for analyzing binding pathways and kinetics, focusing on the extraction of computational features from multiple user runs.

We develop simulations of biomolecular binding via an interactive collaborative interface that harnesses and integrates multi-user exploration of the energetic landscape through haptic interfaces. This addresses the current limitations of molecular docking simulations by facilitating search in the high-dimensional energetic landscape of molecular docking.

Funding Information:

Funded by the National Science Foundation: Award number IIS-1716195.

Publications:

Chavez, Anna and Adamson, Torin and Tapia, Lydia and Jacobson, Bruna "A Mobile Game for Crowdsourced Molecular Docking Pathways" MIG '19: Motion, Interaction and Games, 2019 10.1145/3359566.3360055

Adamson, Torin and Camarena, Julian Antolin and Tapia, Lydia and Jacobson, Bruna "Optimizing Low Energy Pathways in Receptor-Ligand Binding with Motion Planning" 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) , 2020 10.1109/BIBM47256.2019.8983169