ArticleProceedings of the National Academy of Sciences of the United States of America2004
FamClash: a method for ranking the activity of engineered enzymes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 73 citations in OpenAlex.
- X-ray-driven chemistry and conformational heterogeneity in atomic resolution crystal structures of bacterial dihydrofolate reductases.bioRxiv : the preprint server for biology · 2023Article
- Learning epistatic interactions from sequence-activity data to predict enantioselectivity.Journal of computer-aided molecular design · 2017Article
- A receptor dependent-4D QSAR approach to predict the activity of mutated enzymes.Scientific reports · 2017Article
- SwiftLib: rapid degenerate-codon-library optimization through dynamic programming.Nucleic acids research · 2015Article
- A divide-and-conquer approach to determine the Pareto frontier for optimization of protein engineering experiments.Proteins · 2012Article
- Article
- Optimization of combinatorial mutagenesis.Journal of computational biology : a journal of computational molecular cell biology · 2011Article
- Exploiting models of molecular evolution to efficiently direct protein engineering.Journal of molecular evolution · 2011Article
- Computational methods for de novo protein design and its applications to the human immunodeficiency virus 1, purine nucleoside phosphorylase, ubiquitin specific protease 7, and histone demethylases.Current drug targets · 2010Review
- Surface sites for engineering allosteric control in proteins.Science (New York, N.Y.) · 2008Article
- STAR: predicting recombination sites from amino acid sequence.BMC bioinformatics · 2006Article
- IPRO: an iterative computational protein library redesign and optimization procedure.Biophysical journal · 2006Article
- Article
- On the conservative nature of intragenic recombination.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
- Evolution and evolvability of proteins in the laboratory.Proceedings of the National Academy of Sciences of the United States of America · 2004Article
- Computationally mapping sequence space to understand evolutionary protein engineering.Biotechnology progressArticle
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4 authors at 1 institution in 1 country.
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Abstract
This article introduces the computational procedure FamClash for analyzing incompatibilities in engineered protein hybrids by using protein family sequence data. All pairs of residue positions in the sequence alignment that conserve the property triplet of charge, volume, and hydrophobicity are first identified, and significant deviations are denoted as residue-residue clashes. This approach moves beyond earlier efforts aimed at solely classifying hybrids as functional or nonfunctional by correlating the rank ordering of these hybrids based on their activity levels. Experimental testing of this approach was performed in parallel to assess the predictive ability of FamClash. As a model system, single-crossover ITCHY (incremental truncation for the creation of hybrid enzymes) libraries were prepared from the Escherichia coli and Bacillus subtilis dihydrofolate reductases, and the activities of functional hybrids were determined. Comparisons of the predicted clash map as a function of crossover position revealed good agreement with activity data, reproducing the observed V shape and matching the location of a local peak in activity.
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