Surface ID: a geometry-aware system for protein molecular surface comparison

Saleh Riahi, Jae Hyeon Lee, Taylor Sorenson, Shuai Wei, Sven Jager, Reza Olfati-Saber, Yanfeng Zhou, Anna Park, Maria Wendt, Hervé Minoux, Yu Qiu

Abstract: A protein can be represented in several forms, including its 1D sequence, 3D atom coordinates, and molecular surface. A protein surface contains rich structural and chemical features directly related to the protein’s function such as its ability to interact with other molecules. While many methods have been developed for comparing the similarity of proteins using the sequence and structural representations, computational methods based on molecular surface representation are limited.