Molecular tetris

Abstract

Many biological processes, including immune recognition, enzyme catalysis, and molecular signaling, which is still an open problem in biological sciences. We present Molecular Tetris, a game in which a player can explore the binding between a protein receptor and ligand. This exploration is similar to the game Tetris with atomic forces guiding best fits between shapes. This game will be utilized for crowdsourced haptic-guided motion planning. Haptic touch devices enable users to feel the interactions of two molecules as they move the ligand into an appropriate binding site on the receptor. We demonstrate the method on a critical piece of human immune response, ligand binding to a Major Histocompatibility Complex (MHC) molecule. Through multiple runs by our users, we construct a global roadmap that finds low energy paths to molecular docking sites. These paths are comparable to a highly-biased roadmap generated by Gaussian sampling around the known bound state. Our users are able to find low energy paths with both a specialized force-feedback device and a commodity game console controller.