ArticleNucleic acids research2008
GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
39 citing papers in PubMed.
- An optimised promoter and signal peptide improves methionine production of a genetically engineeredFrontiers in microbiology · 2025Article
- Sampling Strategies for Experimentally Mapping Molecular Fitness Landscapes Using High-Throughput Methods.Journal of molecular evolution · 2024Article
- Making Enzymes Suitable for Organic Chemistry by Rational Protein Design.Chembiochem : a European journal of chemical biology · 2022Review
- Multivalent designed proteins neutralize SARS-CoV-2 variants of concern and confer protection against infection in mice.Science translational medicine · 2022Article
- Learning Strategies in Protein Directed Evolution.Methods in molecular biology (Clifton, N.J.) · 2022Review
- A single point mutation converts a glutaryl-7-aminocephalosporanic acid acylase into an N-acyl-homoserine lactone acylase.Biotechnology letters · 2021Article
- Heterologous Expression, Engineering and Characterization of a Novel Laccase ofJournal of fungi (Basel, Switzerland) · 2021Article
- Design of an improved universal signal peptide based on the α-factor mating secretion signal for enzyme production in yeast.Cellular and molecular life sciences : CMLS · 2021Article
- Engineering theFrontiers in pharmacology · 2021Article
- Article
- Reversal of Regioselectivity in Zinc-Dependent Medium-Chain Alcohol Dehydrogenase from Rhodococcus erythropolis toward Octanone Derivatives.Chembiochem : a European journal of chemical biology · 2020Article
- Article
- Predicting Drug Resistance Using Deep Mutational Scanning.Molecules (Basel, Switzerland) · 2020Review
- Protein Farnesyltransferase Catalyzes Unanticipated Farnesylation and Geranylgeranylation of Shortened Target Sequences.Biochemistry · 2020Article
- A 96-multiplex capillary electrophoresis screening platform for product based evolution of P450 BM3.Scientific reports · 2019Article
- Engineered Aminoacyl-tRNA Synthetases with Improved Selectivity toward Noncanonical Amino Acids.ACS chemical biology · 2019Article
- Cognizance of Molecular Methods for the Generation of Mutagenic Phage Display Antibody Libraries for Affinity Maturation.International journal of molecular sciences · 2019Review
- SAMURAI (Solid-phase Assisted Mutagenesis by Uracil Restriction for Accurate Integration) for antibody affinity maturation and paratope mapping.Nucleic acids research · 2019Article
- Applications of Protein Engineering and Directed Evolution in Plant Research.Plant physiology · 2019Review
- Comparative analysis of mutational robustness of the intrinsically disordered viral protein VPg and of its interactor eIF4E.PloS one · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
There are many methods for introducing random mutations into nucleic acid sequences. Previously, we described a suite of programmes for estimating the completeness and diversity of randomized DNA libraries generated by a number of these protocols. Our programmes suggested some empirical guidelines for library design; however, no information was provided regarding library diversity at the protein (rather than DNA) level. We have now updated our web server, enabling analysis of translated libraries constructed by site-saturation mutagenesis and error-prone PCR (epPCR). We introduce GLUE-Including Translation (GLUE-IT), which finds the expected amino acid completeness of libraries in which up to six codons have been independently varied (according to any user-specified randomization scheme). We provide two tools for assisting with experimental design: CodonCalculator, for assessing amino acids corresponding to given randomized codons; and AA-Calculator, for finding degenerate codons that encode user-specified sets of amino acids. We also present PEDEL-AA, which calculates amino acid statistics for libraries generated by epPCR. Input includes the parent sequence, overall mutation rate, library size, indel rates and a nucleotide mutation matrix. Output includes amino acid completeness and diversity statistics, and the number and length distribution of sequences truncated by premature termination codons. The web interfaces are available at http://guinevere.otago.ac.nz/stats.html.
Indexed as
Identifiers
What OpenQuestion holds
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.