ArticleProteins2016
ScaffoldSeq: Software for characterization of directed evolution populations.
Article in Proteins, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
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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
9 citing papers in PubMed, 15 citations in OpenAlex.
- High-throughput screening for class I peptide MHC binding via yeast surface display.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- VesicleVoyager: In Vivo Selection of Surface Displayed Proteins That Direct Extracellular Vesicles to Tissue-Specific Targets.Journal of extracellular vesicles · 2025Article
- Pharmacophore-driven antibody discovery on the yeast surface.bioRxiv : the preprint server for biology · 2025Article
- Molecular Determinants of Affinity and Isoform Selectivity in Protein─Small Molecule Hybrid Inhibitors of Carbonic Anhydrase.Bioconjugate chemistry · 2025Article
- Hyperstable Synthetic Mini-Proteins as Effective Ligand Scaffolds.ACS synthetic biology · 2023Article
- Biophysical Characterization Platform Informs Protein Scaffold Evolvability.ACS combinatorial science · 2019Article
- Constrained Combinatorial Libraries of Gp2 Proteins Enhance Discovery of PD-L1 Binders.ACS combinatorial science · 2018Article
- Deep sequencing methods for protein engineering and design.Current opinion in structural biology · 2017Review
- A Gradient of Sitewise Diversity Promotes Evolutionary Fitness for Binder Discovery in a Three-Helix Bundle Protein Scaffold.Biochemistry · 2017Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
ScaffoldSeq is software designed for the numerous applications-including directed evolution analysis-in which a user generates a population of DNA sequences encoding for partially diverse proteins with related functions and would like to characterize the single site and pairwise amino acid frequencies across the population. A common scenario for enzyme maturation, antibody screening, and alternative scaffold engineering involves naïve and evolved populations that contain diversified regions, varying in both sequence and length, within a conserved framework. Analyzing the diversified regions of such populations is facilitated by high-throughput sequencing platforms; however, length variability within these regions (e.g., antibody CDRs) encumbers the alignment process. To overcome this challenge, the ScaffoldSeq algorithm takes advantage of conserved framework sequences to quickly identify diverse regions. Beyond this, unintended biases in sequence frequency are generated throughout the experimental workflow required to evolve and isolate clones of interest prior to DNA sequencing. ScaffoldSeq software uniquely handles this issue by providing tools to quantify and remove background sequences, cluster similar protein families, and dampen the impact of dominant clones. The software produces graphical and tabular summaries for each region of interest, allowing users to evaluate diversity in a site-specific manner as well as identify epistatic pairwise interactions. The code and detailed information are freely available at http://research.cems.umn.edu/hackel. Proteins 2016; 84:869-874. © 2016 Wiley Periodicals, Inc.
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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.