Welcome to Xiaoqiang Huang's Homepage!
Xiaoqiang Huang, PhD
Postdoctoral Research Fellow
Department of Computational Medicine and Bioinformatics
Medical School, University of Michigan
100 Washtenaw Avenue
Ann Arbor, MI 48109‐2218, USA
Computational Biology, Bioinformatics, De Novo Computational Protein/Enzyme Design, Molecular
Modeling, Biophysics, Machine Learning and Deep Learning, Algorithms, Molecular Docking,
Protein/Enzyme Evolution, Protein‐Protein Interactions, Protein‐Ligand Interactions and related
PhD, Chemical Engineering, Tsinghua University, Beijing, China, 2017
Concentrations: Matching algorithm, molecular modeling, computational protein/enzyme design
Dissertation: Protein scaffold selection and computational design of cephradine synthase
- MS, Chemical Engineering, Tsinghua University, Beijing, China, 2014
Concentrations: Deterministic optimization algorithm, molecular modeling, computation
Dissertation: Study on molecular modeling and optimization algorithm in computational enzyme design
- BS, Chemical Engineering, Tsinghua University, Beijing, China, 2010
Concentrations: Computation protein/enzyme design, bioactive ligand pose generation
Thesis: Study on placement of small-molecule ligand conformations for computational redesign of
2‐deoxyribose‐5‐phosphate aldolase in preparation of atorvastatin
Research Experience at the Yang Zhang Lab
Postdoctoral Research Fellow, University of Michigan, 2017.9 ~ Now
- Developed accurate and fast physical energy functions (EvoEF and EvoEF2) for de novo protein
design scoring and involved in extending the EvoDesign protocol from monomer design to protein‐protein interaction design.
- Involved in completely redesign of BIR3 domain of the X-linked Inhibitor of Apoptosis Protein (XIAP) to change the apoptosis pathway.
- Developed a method, SSIPe, for accurate binding affinity change prediction upon mutations, which is important in protein/enzyme engineering and designing new therapeutics to target protein-protein interaction related diseases.
- Quantitatively assessed the impact of rotamer libraries on protein side-chain prediction and protein design using EvoEF2 and simulated-annealing Monte Carlo based searching algorithm.
- Extending EvoDesign into EvoDesign2 by optimizing the architecture and speed.
- Developing a fast and accurate algorithm for side-chain packing (FASPR).
- Developing a novel efficient matching algorithm to select novel protein scaffold for de novo enzyme design.
- Computational de novo design of PD-L1 and VEGFR inhibitors to change apoptosis pathway to target cancer.
Xiaoqiang Huang, Robin Pearce, Yang Zhang. Toward the accuracy and speed of protein side-chain packing: a systematic study on rotamer libraries. (submitted)
Xiaoqiang Huang, Wei Zheng, Robin Pearce, Yang Zhang. SSIPe: Accurately estimating protein-protein binding affinity change upon SNP mutations using evolutionary profiles in combination with an optimized physical energy function. (under revision)
Xiaoqiang Huang, Robin Pearce, Yang Zhang. EvoEF2: Accurate and fast energy function for computational protein design. Bioinformatics (2019) (Accepted)
Robin Pearce†, Xiaoqiang Huang†, Dani Setiawan, Yang Zhang. EvoDesign: Designing Protein–Protein Binding Interactions Using Evolutionary Interface Profiles in Conjunction with an Optimized Physical Energy Function. Journal of Molecular Biology (2019) 431: 2467-2476. (†: co-first author)
David Shultis, Pralay Mitra, Xiaoqiang Huang, Jarrett Johnson, Naureen Aslam Khattak, Felicia Gray, Clint Piper, Jeff Czajka, Logan Hansen, Bingbing Wan, Krishnapriya Chinnaswamy, Liu Liu, Mi Wang, Jingxi Pan, Jeanne Stuckey, Tomasz Cierpicki, Christoph H. Borchers, Shaomeng Wang, Ming Lei, Yang Zhang. Changing the Apoptosis Pathway through Evolutionary Protein Design. Journal of Molecular Biology (2019) 431: 825-841.
Jing Xue, Xiaoqiang Huang, Yushan Zhu. Using molecular dynamics simulations to evaluate active designs of cephradine hydrolase by molecular mechanics/Poisson–Boltzmann surface area and molecular mechanics/generalized Born surface area methods. RSC Advances (2019) 9: 13868-13877.
Jinwen He†, Xiaoqiang Huang†, J Xue, Yushan Zhu. Computational redesign of penicillin acylase for cephradine synthesis with high kinetic selectivity. Green Chemistry (2018) 20: 5484-5490. (†: co-first author)
Xiaoqiang Huang, Jing Xue, Yushan Zhu. Computational design of cephradine synthase in a new scaffold identified from structural databases. Chemical Communications (2017) 53: 7604-7607.
Ye Tian, Zhaobin Xu, Xiaoqiang Huang, Yushan Zhu. Computational design to improve catalytic activity of cephalosporin C acylase from Pseudomonas strain N176. RSC Advances (2017) 7: 30370-30375.
Ye Tian, Xiaoqiang Huang, Qing Li, Yushan Zhu. Computational design of variants for cephalosporin C acylase from Pseudomonas strain N176 with improved stability and activity. Applied microbiology and biotechnology (2017) 101: 621-632.
Xiaoqiang Huang, Jing Xue, Min Lin, Yushan Zhu. Use of an improved matching algorithm to select scaffolds for enzyme design based on a complex active site model. PLoS ONE (2016) 11(5): e0156559.
Jing Xue, Xiaoqiang Huang, Min Lin, Yushan Zhu. A fast loop-closure algorithm to accelerate residue matching in computational enzyme design. Journal of Molecular Modeling (2016) 22: 49.
Ye Tian, Xiaoqiang Huang, Yushan Zhu. Computational design of enzyme-ligand binding using a combined energy function and deterministic sequence optimization algorithm. Journal of Molecular Modeling (2015) 21: 191.
Xiaoqiang Huang, Jing Xue, Yulin Lei, Ye Tian, Yushan Zhu. ProdaMatch: a matching algorithm for catalytic sites selection in de novo computational enzyme design. The 13th National Symposium of Computer and Computational Chemistry (2015) Guangzhou, China.
Qing Li, Xiaoqiang Huang, Yushan Zhu. Evaluation of active designs of cephalosporin C acylase by molecular dynamics simulation and molecular docking. Journal of Molecular Modeling (2014) 20: 2314.
Xiaoqiang Huang, Kehang Han, Yushan Zhu. Systematic optimization model and algorithm for binding sequence selection in computational enzyme design. Protein Science (2013) 22: 929-941.
Xiaoqiang Huang, Ji Yang, Yushan Zhu. A solvated ligand rotamer approach and its application in computational protein design. Journal of Molecular Modeling (2013) 19: 1355-1367.
Xiaoqiang Huang, Yushan Zhu. Design of 2-deoxyribose-5-phosphate aldolase in preparation of atorvastatin side chain. International Graduate Forum on Biotechnology, Bioengineering and Biomedical Science (2011) Beijing, China.
Yushan Zhu, Xiaoqiang Huang, Jinwen He. Cephradine synthase mutant and coding gene thereof. CN Patent CN107099523 A.
Yushan Zhu, Ye Tian, Xiaoqiang Huang. Cephalosporin acylase mutant and coding gene and application thereof. CN Patent CN106119233 A.