ReviewBioorganic & medicinal chemistry2017
Aligator: A computational tool for optimizing total chemical synthesis of large proteins.
Review in Bioorganic & medicinal chemistry, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
11 citing papers in PubMed.
- Total chemical synthesis of pentameric cholera toxin subunit B.Chemical communications (Cambridge, England) · 2026Article
- BracketMaker: Visualization and optimization of chemical protein synthesis.Protein science : a publication of the Protein Society · 2024Article
- D-Peptide and D-Protein Technology: Recent Advances, Challenges, and Opportunities.Chembiochem : a European journal of chemical biology · 2023Review
- Improved Handling of Peptide Segments Using Side Chain-Based "Helping Hand" Solubilizing Tools.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Traceless Click-Assisted Native Chemical Ligation Enabled by Protecting Dibenzocyclooctyne from Acid-Mediated Rearrangement with Copper(I).Bioconjugate chemistry · 2021Article
- A glutamic acid-based traceless linker to address challenging chemical protein syntheses.Organic & biomolecular chemistry · 2021Article
- Deciphering protein post-translational modifications using chemical biology tools.Nature reviews. Chemistry · 2020Review
- Enhancing native chemical ligation for challenging chemical protein syntheses.Current opinion in chemical biology · 2020Review
- Design, synthesis and characterization of structurally dynamic cyclic N,S-acetals.Chemical communications (Cambridge, England) · 2020Article
- Advancing the Frontiers of Chemical Protein Synthesis-The 7Cell chemical biology · 2018Article
- Mirror-image polymerase chain reaction.Cell discovery · 2017Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The scope of chemical protein synthesis (CPS) continues to expand, driven primarily by advances in chemical ligation tools (e.g., reversible solubilizing groups and novel ligation chemistries). However, the design of an optimal synthesis route can be an arduous and fickle task due to the large number of theoretically possible, and in many cases problematic, synthetic strategies. In this perspective, we highlight recent CPS tool advances and then introduce a new and easy-to-use program, Aligator (Automated Ligator), for analyzing and designing the most efficient strategies for constructing large targets using CPS. As a model set, we selected the E. coli ribosomal proteins and associated factors for computational analysis. Aligator systematically scores and ranks all feasible synthetic strategies for a particular CPS target. The Aligator script methodically evaluates potential peptide segments for a target using a scoring function that includes solubility, ligation site quality, segment lengths, and number of ligations to provide a ranked list of potential synthetic strategies. We demonstrate the utility of Aligator by analyzing three recent CPS projects from our lab: TNFα (157 aa), GroES (97 aa), and DapA (312 aa). As the limits of CPS are extended, we expect that computational tools will play an increasingly important role in the efficient execution of ambitious CPS projects such as production of a mirror-image ribosome.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.