Recent advances in automated protein design and its future challenges
Open accessAbstract
INTRODUCTION: Protein function is determined by protein structure which is in turn determined by the corresponding protein sequence. If the rules that cause a protein to adopt a particular structure are understood, it should be possible to refine or even redefine the function of a protein by working backwards from the desired structure to the sequence. Automated protein design attempts to calculate the effects of mutations computationally with the goal of more radical or complex transformations than are accessible by experimental techniques. Areas covered: The authors give a brief overview of the recent methodological advances in computer-aided protein design, showing how methodological choices affect final design and how automated protein design can be used to address problems considered beyond traditional protein engineering, including the creation of novel protein scaffolds for drug development. Also, the authors address specifically the future challenges in the development of automated protein design. Expert opinion: Automated protein design holds potential as a protein engineering technique, particularly in cases where screening by combinatorial mutagenesis is problematic. Considering solubility and immunogenicity issues, automated protein design is initially more likely to make an impact as a research tool for exploring basic biology in drug discovery than in the design of protein biologics.
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Quantum annealing is suitable to the problem of protein design, i.e. finding the amino acid sequence that minimizes the energy of a chosen main-chain configuration.
“Quantum annealing is also suitable to the problem of protein design [43, 77, 78], i.e. finding the amino acid sequence that minimizes the energy of a chosen main-chain configuration.”
From Quantum computing algorithms: getting closer to critical problems in computational biology (2022) · cites this paper as [78]
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Kozlova, E., Valentin, A., Khadhraoui, A., & Gutierrez, D. N.-Z. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.09.25.559346 · Cited by 4 · see citing works
Protein Engineering of DNA-Dependent Enzymes
Yudkina, A. V., & Zharkov, D. O. (2020) · Advances in experimental medicine and biology · doi:10.1007/978-3-030-41283-8_2 · Cited by 2 · see citing works
EvoProDom: evolutionary modeling of protein families by assessing translocations of protein domains
Carmi, G., Gorohovski, A., & Frenkel‐Morgenstern, M. (2021) · FEBS Open Bio · doi:10.1002/2211-5463.13245 · Cited by 1 · see citing works
Artificial intelligence for CRISPR-based biosensing: From molecular design to assay intelligence
Wang, R., Zhang, Q., Gaira, S., Zhao, Y., Lai, J., Li, M., Zhang, C., Wu, L., Deng, F., & Tang, S. (2026) · TrAC Trends in Analytical Chemistry · doi:10.1016/j.trac.2026.119061 · Cited by 1 · see citing works
Evolutionary Modeling of Protein Families by Chromosomal Translocation Events
Carmi, G., Gorohovski, A., & Frenkel‐Morgenstern, M. (2021) · Elsevier eBooks · doi:10.1016/b978-0-323-90752-1.00003-1
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- Authors
- Setiawan, D., Brender, J., & Zhang, Y.
- Affiliations
- University of Michigan (US)
- National Cancer Institute (US)
- Corresponding author
- Zhang, Yang
- Venue
- Expert Opinion on Drug Discovery
- Publisher
- Informa UK Limited
- Published
- 2018-04-25
- Volume
- 13
- Issue
- 7
- Pages
- 587-604
- ISSN
- 1746-0441 (ISSN-L)
- 1746-045X
- PMC
- PMC6002944
- OpenAlex
- W2800570933
- Cited by
- 26
- References
- 195
- Citations by year
- 2026: 2 · 2025: 1 · 2024: 2 · 2023: 7 · 2022: 3 · 2021: 5 · 2020: 2 · 2019: 3 · 2018: 1
- FWCI
- 0.27
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Expert Opinion on Drug Discovery (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Division of Biological Infrastructure (NSF 1564756)
- National Institute of General Medical Sciences (R01 GM083107,R01 GM116960)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chemical Synthesis and Analysis
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- protein engineering, protein structure-function relationship, protein scaffolds, drug development, combinatorial mutagenesis, protein solubility, immunogenicity
- MeSH terms
- Amino Acid Sequence, Animals, Automation, Humans, Protein Conformation, Proteins, Solubility, Drug Design, Protein Engineering, Computer-Aided Design, Drug Discovery
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