I will present our recent work on protein docking and design. First, we optimized our docking algorithm with a new fast Fourier transform library and molecular positioning, leading to on average an 8.5 fold improvement in computational speed while maintaining the same accuracy. Second, we explored angular distance for improving docking efficiency and clustering. We developed a hybrid-resolution approach based on angular distance, which led to a six-fold improvement in computational speed while maintaining the same accuracy. We can combine the above two improvements and yield a docking algorithm that is 50 times faster than before. Third, we developed a new T cell receptor (TCR) docking algorithm called TCRFlexDock and a new benchmark containing 20 unique TCR/MHC-peptide complexes for which unbound structures are also available. Finally, we developed a new scoring function called ZAPP for predicting of protein-protein binding affinities based on the structures of the unbound components and the complex.

Zhipeng Weng graduated from the University of Science & Technology of China with a B.S. in Electrical Engineering. She received her PhD from the Graduate Program in Biomedical Engineering at Boston University. The focus of her thesis research was in computational biology, specifically on calculating binding free energies of protein-protein interactions. Dr. Weng’s current research focuses on computational analysis of transcriptional regulation. She has started to study epogenomics and nucleosome positioning, which play important roles in transcriptional regulation. In addition, she is investigating the function and regulation of small RNAs in metazoan. Dr. Weng is a full professor, with tenure in the Department of Biochemistry & Molecular Pharmacology at the University of Massachusetts Medical School. She also serves as Director and Professor of the Program in Bioinformatics and Integrative Biology.