ArticleBioinformatics (Oxford, England)2021
CoLiDe: Combinatorial Library Design tool for probing protein sequence space.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Lignonaut: designing diverse combinatorial libraries for the exploration and annotation of lignin oligomer spaces.Journal of cheminformatics · 2026Article
- Article
- GGAssembler: Precise and economical design and synthesis of combinatorial mutation libraries.Protein science : a publication of the Protein Society · 2024Article
- Modern and prebiotic amino acids support distinct structural profiles in proteins.Open biology · 2022Article
- Sequencing the origins of life.BBA advances · 2022Review
- Building the SynBio community in the Czech Republic from the bottom up: You get what you give.Biotechnology notes (Amsterdam, Netherlands) · 2022Article
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Authors and funding
5 authors.
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Abstract
motivationCurrent techniques of protein engineering focus mostly on re-designing small targeted regions or defined structural scaffolds rather than constructing combinatorial libraries of versatile compositions and lengths. This is a missed opportunity because combinatorial libraries are emerging as a vital source of novel functional proteins and are of interest in diverse research areas.
resultsHere, we present a computational tool for Combinatorial Library Design (CoLiDe) offering precise control over protein sequence composition, length and diversity. The algorithm uses evolutionary approach to provide solutions to combinatorial libraries of degenerate DNA templates. We demonstrate its performance and precision using four different input alphabet distribution on different sequence lengths. In addition, a model design and experimental pipeline for protein library expression and purification is presented, providing a proof-of-concept that our protocol can be used to prepare purified protein library samples of up to 1011-1012 unique sequences. CoLiDe presents a composition-centric approach to protein design towards different functional phenomena. AVAILABILITYAND IMPLEMENTATION: CoLiDe is implemented in Python and freely available at https://github.com/voracva1/CoLiDe. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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