Yang Shen

Assistant Professor

Yang Shen

Office: WEB 223A
Phone: 979.862.1694
Fax: 979.845.6259
Email: yshen@tamu.edu

Personal Website
Google Scholar Profile

Research Interests

Modeling, simulation, and engineering of biomolecules and biomolecular systems.
• Computational Molecular Biology
- Structural prediction of protein interactions
- Drug design
• Computational Systems Biology
- Systems therapeutics
- Synthetic biology
• Bioinformatics
• Optimization and learning
• Systems and control


  • Ph.D., Systems Engineering, Boston University, 2008
  • B.E., Automation, University of Science and Technology of China, 2002

Selected Publications

Molecular Mechanisms and Design Principles for Promiscuous Inhibitors to Avoid Drug Resistance: Lessons Learned from HIV‐1 Protease Inhibition Y Shen, ML Radhakrishnan, B Tidorm Proteins: Structure, Function, and Bioinformatics 2014

Modulators of resistant androgen receptor MD Balbas, MJ Evans, CL Sawyers, Y Shen, D Hosfield, GL Greenem US Patent WO/2014/066,799m 2014

Blind Prediction of Interfacial Water Positions in CAPRI MF Lensink, IH Moal, PA Bates, PL Kastritis, AS Melquiond, E Karaca, .., Proteins: Structure, Function and Bioinformatics 9 2014

ESR1 ligand-binding domain mutations in hormone-resistant breast cancer W Toy, Y Shen, H Won, B Green, RA Sakr, M Will, Z Li, K Gala, S Fanning, ..., Nature genetics 45 (12), 1439–1445 61 2013

Improved flexible refinement of protein docking in CAPRI rounds 22–27 Y Shen, Proteins: Structure, Function, and Bioinformatics 81 (12), 2129–2136 3 2013

Testing the Substrate-Envelope Hypothesis with Designed Pairs of Compounds Y Shen, MD Altman, A Ali, MNL Nalam, H Cao, TM Rana, CA Schiffer, ..., ACS Chemical Biology 8 (11), 2433–2441 2013

Overcoming mutation-based resistance to antiandrogens with rational drug design MD Balbas, MJ Evans, DJ Hosfield, J Wongvipat, VK Arora, PA Watson, ..., eLife 2, e00499 64 2013

Charge Optimization Theory for Induced-Fit Ligands Y Shen, MK Gilson, B Tidor, Journal of Chemical Theory and Computation 8 (11), 4580-4592 3 2012

Identification of Druggable Hot Spots on Proteins and in Protein–Protein Interfaces D Beglov, R Brenke, GY Chuang, D Hall, M Landon, CH Ngan, Y Shen, ..., Computational Protein-Protein Interactions, 253 2010

Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13–19, D Kozakov, DR Hall, D Beglov, R Brenke, SR Comeau, Y Shen, K Li, ..., Proteins: Structure, Function, and Bioinformatics 78 (15), 3124-3130