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Welcome to Xiaoqiang Huang's Homepage!

Xiaoqiang Huang, PhD
Research Investigator
Department of Computational Medicine and Bioinformatics
Medical School, University of Michigan
100 Washtenaw Avenue
Ann Arbor, MI 48109‐2218, USA
Tel: (734)‐647‐1646
Email: xiaoqiah@umich.edu


Research Interests

• Protein Design and Protein Engineering
  
• Enzyme Design and Enzyme Engineering
  

Education

• PhD, Chemical Engineering, Tsinghua University, 2017
• MS, Chemical Engineering, Tsinghua University, 2014
• BS, Chemical Engineering, Tsinghua University, 2010

Research in the Yang Zhang Lab

• Developed accurate and fast physical energy function for de novo protein design (The EvoEF series) [server]
• Extended the EvoDesign protocol from monomer design to protein‐protein interaction (PPI) design [server]
• Involved in completely redesign of BIR3 domain of the X-linked Inhibitor of Apoptosis Protein (XIAP) to change the apoptosis pathway [paper] [SI]
• Developed SSIPe for accurate binding affinity change prediction upon mutations at protein-protein interface [server]
• Assessed the impact of rotamer libraries on protein side-chain modeling using EvoEF2 and simulated annealing optimization [paper] [SI]
• Developing a fast, accurate and deterministic method for side-chain packing (FASPR) [server]
• Optimizing the scoring function, searching engine and computational efficiency of EvoDesign [server]
• De novo design of peptide inhibitors to block the association of SARS-CoV-2 Spike and human ACE2 [paper]
• Designing Nanobody-based biosensors to detect toxic Aflatoxin B1: a study on protein-ligand interaction design

Publications [Google Scholar Profile]

• E Ong, X Huang, R Pearce, Y Zhang, Y He. Computational Design of SARS-CoV-2 Spike Glycoproteins to Increase Immunogenicity by T Cell Epitope Engineering. Computational and Structural Biotechnology Journal. In press. (co-first author)
• X Huang, C Zhang, R Pearce, GS Omenn, Y Zhang. Identifying the Zoonotic Origin of SARS-CoV-2 by Modeling the Binding Affinity Between the Spike Receptor-Binding Domain and Host ACE2. Journal of Proteome Research (2020) 19:4844-4856.
• S Wu, C Tian, P Liu, D Guo, W Zheng, X Huang, Y Zhang, L Liu. Effects of SARS‐CoV‐2 mutations on protein structures and intraviral protein‐protein interactions. Journal of Medical Virology (2020) DOI: 10.1002/jmv.26597.
• MH Madina, MS Rahman, X Huang, Y Zhang, H Zheng, H Germain. A Poplar Rust Effector Protein Associates with Protein Disulfide Isomerase and Enhances Plant Susceptibility. Biology (2020) 9:294.
• X Huang, R Pearce, Y Zhang. De novo design of protein peptides to block association of the SARS-CoV-2 spike protein with human ACE2. Aging (2020) 12:11263-11276.
• Z Tu, X Huang, J Fu, N Hu, W Zheng, Y Li, Y Zhang. Landscape of Variable Domain of Heavy‐chain‐only Antibody Repertoire from Alpaca. Immunology (2020) 161:53–65.
• X Huang, R Pearce, Y Zhang. FASPR: an open-source tool for fast and accurate protein side-chain packing. Bioinformatics (2020) 36:3758-3765.
• C Zhang, W Zheng, X Huang, EW Bell, X Zhou, Y Zhang. Protein structure and sequence reanalysis of 2019-nCoV genome refutes snakes as its intermediate host and the unique similarity between its spike protein insertions and HIV-1. Journal of Proteome Research (2020) 19:1351-1360.
• X Huang, R Pearce, Y Zhang. Toward the accuracy and speed of protein side-chain packing: a systematic study on rotamer libraries. Journal of Chemical Information and Modeling (2020) 60:410-420.
• X Huang, W Zheng, R Pearce, Y Zhang. SSIPe: accurately estimating protein-protein binding affinity change upon mutations using evolutionary profiles in combination with an optimized physical energy function. Bioinformatics (2019) 36:2429-2437.
• X Huang, R Pearce, Y Zhang. EvoEF2: accurate and fast energy function for computational protein design. Bioinformatics (2020) 36:1135-1142.
• R Pearce, X Huang, D Setiawan, Y 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)
• D Shultis, P Mitra, X Huang, J Johnson, NA Khattak, F Gray, C Piper, ..., Y Zhang. Changing the Apoptosis Pathway through Evolutionary Protein Design. Journal of Molecular Biology (2019) 431:825-841.
• J Xue, X Huang, Y 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.
• J He, X Huang, J Xue, Y Zhu. Computational redesign of penicillin acylase for cephradine synthesis with high kinetic selectivity. Green Chemistry (2018) 20:5484-5490. (co-first author)
• X Huang, J Xue, Y Zhu. Computational design of cephradine synthase in a new scaffold identified from structural databases. Chemical Communications (2017) 53:7604-7607.
• Y Tian, Z Xu, X Huang, Y Zhu. Computational design to improve catalytic activity of cephalosporin C acylase from Pseudomonas strain N176. RSC Advances (2017) 7:30370-30375.
• Y Tian, X Huang, Q Li, Y 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.
• X Huang, J Xue, M Lin, Y Zhu. Use of an improved matching algorithm to select scaffolds for enzyme design based on a complex active site model. PLoS ONE (2016) 11:e0156559.
• J Xue, X Huang, M Lin, Y Zhu. A fast loop-closure algorithm to accelerate residue matching in computational enzyme design. Journal of Molecular Modeling (2016) 22:49.
• Y Tian, X Huang, Y Zhu. Computational design of enzyme-ligand binding using a combined energy function and deterministic sequence optimization algorithm. Journal of Molecular Modeling (2015) 21:191.
• Q Li, X Huang, Y Zhu. Evaluation of active designs of cephalosporin C acylase by molecular dynamics simulation and molecular docking. Journal of Molecular Modeling (2014) 20:2314.
• X Huang, K Han, Y Zhu. Systematic optimization model and algorithm for binding sequence selection in computational enzyme design. Protein Science (2013) 22:929-941.
• X Huang, J Yang, Y Zhu. A solvated ligand rotamer approach and its application in computational protein design. Journal of Molecular Modeling (2013) 19:1355-1367.