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BioLiP E. coli GLASS GPCR-HGmod GPCR-RD GPCR-EXP Tara-3D TM-fold DECOYS POTENTIAL RW/RWplus EvoEF HPSF THE-DB ADDRESS Alpaca-Antibody CASP7 CASP8 CASP9 CASP10 CASP11 CASP12 CASP13 CASP14


Robin Pearce

Ph.D. Student, Department of Computational Medicine and Bioinformatics
Google Scholar Profile

Contact
    RM 2035B, Palmer Commons
    100 Washtenaw Ave
    Ann Arbor, MI 48109-2218
    robpearc@umich.edu
Education
  • 2019-Present, Ph.D. in Bioinformatics, University of Michigan, Ann Arbor, MI
  • 2017-2018, M.S. in Biological Chemistry, University of Michigan, Ann Arbor, MI
  • 2017-2018, M.S.E. in Biomedical Engineering, University of Michigan, Ann Arbor, MI
  • 2014-2017, B.S.E. in Biomedical Engineering, University of Michigan, Ann Arbor, MI
Research Interests
  • Algorithm development for protein design and structure prediction
  • Development of protein-based therapeutics using computational protein design
Publications
  • Pearce, R. and Zhang, Y. (2021) Deep learning techniques have significantly impacted protein structure prediction and protein design. Curr. Opin. Struct. Biol., 68: 194-207.
  • Zhang, B., Zhang, W., Pearce, R., Zhang, Y., and Shen HB. (2021) Fitting Low-Resolution Protein Structures into Cryo-EM Density Maps by Multiobjective Optimization of Global and Local Correlations. J. Phys. Chem. B, 125: 528-538.
  • Ong, E., Huang, X., Pearce, R., Zhang, Y., He, Y. (2021) Computational design of SARS-CoV-2 spike glycoproteins to increase immunogenicity by T cell epitope engineering. Comput. Struct. Biotechnol. J., 19: 518-529.
  • Huang, X., Zhang, C., Pearce, R., Omenn, GS., and Zhang, Y. (2020) Identifying the Zoonotic Origin of SARS-CoV-2 by Modeling the Binding Affinity between the Spike Receptor-Binding Domain and Host ACE2. . Proteome Res., 19: 4844-4856.
  • Huang, X., Pearce, R., Zhang, Y. (2020) Computational Design of Peptides to Block Binding of the SARS-CoV-2 Spike Protein to Human ACE2. Aging, 12: 11263-11276.
  • Zhang, B., Zhang, X., Pearce, R., Shen, HB., Zhang, Y. (2020) A new protocol for atomic-level protein structure modeling and refinment using low-to-medium resolution cryo-EM density maps. Journal of Molecular Biology, 432: 5365-5377.
  • Huang, X., Pearce, R., Zhang, Y. (2020) FASPR: an open-source tool for fast and accurate protein side-chain packing. Bioinformatics, 36: 3758–3765.
  • Liu, X., Liu, J., Zhang, W., Pearce, R., Chen, M., Zhang, T., Liu, B. (2020) Effect of the Degree of Glycation on the Stability and Aggregation of Bovine Serum Albumin. Food Hydrocolloids, 106: 105892.
  • Zheng, W., Zhou, X., Wuyun, Q., Pearce, R., Li, Y., Zhang, Y. (2020) FUpred: Detecting protein domains through deep-learning based contact map prediction. Bioinformatics, 36: 3749–3757.
  • Liu, X., Zhang, W., Liu, J., Pearce, R., Zhang, Y., Zhang, K., Ruan, Q., Yu, Y., Liu, B. (2020) Mg2+ inhibits heat-induced aggregation of BSA: the mechanism and its binding site. Food Hydrocolloids, 101, 105450.
  • Huang, X., Pearce, R., Zhang, Y. (2020) EvoEF2: Accurate and fast energy function for computational protein design. Bioinformatics, 36(4), 1135-1142.
  • Huang, X., Zheng, W., Pearce, R., Zhang, Y. (2019) SSIPe: Accurately estimating protein-protein binding affinity change upon SNP mutations using evolutionary profiles in combination with an optimized physical energy function. Bioinformatics, 36: 2429-2437.
  • Huang, X., Pearce, R., Zhang, Y. (2019) Toward the accuracy and speed of protein side-chain packing: a systematic study on rotamer libraries. Journal of Chemical Informatics and Modeling, 60(1), 410-420.
  • Zheng, W., Wuyun, Q., Li, Y., Mortuza, SM., Zhang, C., Pearce, R., Ruan, J., Zhang, Y. (2019) Detecting distant-homology protein structures by aligning deep neural-network based contact maps. PLOS Computational Biology, 15(10): e1007411.
  • Oraiqat, I., DeBruin, S., Pearce, R., Como, C., Mikell, J., Taylor, C., Way, J., Suarez, M., Rehemtulla, A., Clarke, R., El Naqa, I. (2019) Silicon Photomultipliers for Deep Tissue Cerenkov Emission Detection During External Beam Radiotherapy. IEEE Photonics Journal 11(4), 1-16.
  • Zheng, W., Li, Y., Zhang, C., Pearce, R., Mortuza, SM., Zhang, Y. (2019) Deep-learning contact-map guided protein structure prediction in CASP13. Proteins: Structure, Function, and Bioinformatics, 82(12), 1149-1164. [Server]
  • Zheng, W., Zhang, C., Wuyun, Q., Pearce, R., Li, Y., Zhang, Y. (2019) LOMETS2: Improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins. Nucleic Acid Research, 47(W1), W429-W436. [Server]
  • Pearce, R., Huang, X., Setiawana, D., Zhang, Y. (2019) EvoDesign: Designing protein-protein binding interactions using evolutionary interface profiles in conjunction with an optimized physical energy function. Journal of Molecular Biology, 431(13), 2467-2476. [PDF]
Oral Presentations at Conferences
  • Pearce, R., Zheng, W., Zhang, C., Li, Y., Mortuza, SM., Zhang, Y. (2018) Zhang Groups: Automated Structure Prediction by C-I-TASSER and C-QUARK in CASP13. 13th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction. Quintana Roo, Mexico.
Conference Abstracts and Papers
  • Zhang, C., Li, Y., Zheng, W., Bell, E., Huang, X., Pearce, R., Zhou, X., and Zhang, Y. (2020) Protein 3D Structure Prediction by D-QUARK in CASP14. 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction. [Abstract]
  • Li, Y., Zheng, W., Zhang, C., Bell, E., Huang, X., Pearce, R., Zhou, X., and Zhang, Y. (2020) Protein 3D Structure Prediction by Zhang Human Group in CASP14. 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction. [Abstract]
  • Li, Y., Zheng, W., Zhang, C., Bell, E., Huang, X., Pearce, R., Zhou, X., and Zhang, Y. (2020) Protein 3D Structure Prediction by D-I-TASSER in CASP14. 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction. [Abstract]
  • Zhang, C., Pearce, R., Zhang, Y. (2019) C-QUARK: contact-assisted de novo protein structure prediction on XSEDE Comet. International Conference on Supercomputing (ICS). Phoenix, AZ. [Abstract]
  • Oraiqat, I., Taylor, C., Como, C., Way, J., Pearce, R., Debruin, S., Clarke, R., El Naqa, I. (2017) A New Approach for Cherenkov Emission Detection Using Silicon Photomultipliers. Proceedings of the 59th Annual Meeting of the American Association of Physicists in Medicine. Denver, CO.
  • Emery, N., Renberg, A., Castillo, C., Nishi, A., Haad, A., Girgis, A., Bernstein, Z., Lewin, D., Kaczmarek, C., Pearce, R., Vobbilisetty, V., Kopyeva, I., Sun, R. (2017) iGEM Report: Kinetic Modeling of a Novel Protein Detection System Using Proximity-Dependent Ligation and Nucleic Acid Sequence-Based Amplification. iGEM PLOS Collections. Boston, MA.
  • Subramanian, C., Pearce, R., Clague, M., Timmermann, B., Cohen, M. (2016) A novel naturally-derived withalonglide synergizes with cisplatin to block self-renewal, migration, and EMT transition to enhance apoptosis via targeting of translational initiation. AACR Translational Control of Cancer: A New Frontier in Cancer Biology and Therapy. San Francisco, CA.
Honors/Awards
  • Valedictorian, Clinton High School, Clinton, MI (2014)
  • Regents Merit Scholarship, University of Michigan (2014)
  • Engineering Scholarship of Honor, University of Michigan (2014-2017)
  • James B. Angell Scholar, University of Michigan (2017)
  • Graduated Summa Cum Laude, Department of Biomedical Engineering, University of Michigan (2017)
  • Rackham Travel Grant, University of Michigan (2018)
  • Advanced Proteome Informatics of Cancer Training Program NCI Pre-doctoral Fellowship, University of Michigan (2019-2021)


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