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Literature DB >> 15857784

Mathematical expressions useful in the construction, description and evaluation of protein libraries.

Abstract

The creation of protein libraries by random mutagenesis and cassette mutagenesis has proven to be a successful method of protein engineering. Appropriate statistical analysis is important for the proper construction of these libraries and even more important for the interpretation of data from these libraries. We present simple mathematical expressions useful in the creation and evaluation of such libraries. These equations are useful in estimating the distribution of mutations, the degeneracy of the library and the frequency of a particular clone in the library. In addition, general equations addressing the probability that a particular clone is in a library, the probability that a library is complete, and as the consequences of retransformation of the library on these probabilities are presented.

Mesh：

Year: 2005 PMID： 15857784 DOI： 10.1016/j.bioeng.2004.11.002

Source DB: PubMed Journal: Biomol Eng ISSN： 1389-0344

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Cited

32 in total

1. When second best is good enough: another probabilistic look at saturation mutagenesis.

Authors: Yuval Nov
Journal: Appl Environ Microbiol Date: 2011-10-28 Impact factor: 4.792

2. Combinatorial reshaping of the Candida antarctica lipase A substrate pocket for enantioselectivity using an extremely condensed library.

Authors: Anders G Sandström; Ylva Wikmark; Karin Engström; Jonas Nyhlén; Jan-E Bäckvall
Journal: Proc Natl Acad Sci U S A Date: 2011-12-16 Impact factor: 11.205

3. Protease specificity determination by using cellular libraries of peptide substrates (CLiPS).

Authors: Kevin T Boulware; Patrick S Daugherty
Journal: Proc Natl Acad Sci U S A Date: 2006-05-03 Impact factor: 11.205

4. Persistence of elevated deamidated gliadin peptide antibodies on a gluten-free diet indicates nonresponsive coeliac disease.

Authors: B N Spatola; K Kaukinen; P Collin; M Mäki; M F Kagnoff; P S Daugherty
Journal: Aliment Pharmacol Ther Date: 2014-01-06 Impact factor: 8.171

Mathematical expressions useful in the construction, description and evaluation of protein libraries.

1. When second best is good enough: another probabilistic look at saturation mutagenesis.

2. Combinatorial reshaping of the Candida antarctica lipase A substrate pocket for enantioselectivity using an extremely condensed library.

3. Protease specificity determination by using cellular libraries of peptide substrates (CLiPS).

4. Persistence of elevated deamidated gliadin peptide antibodies on a gluten-free diet indicates nonresponsive coeliac disease.

5. Systematic exploration of active site mutations on human deoxycytidine kinase substrate specificity.

6. Mutations in adenine-binding pockets enhance catalytic properties of NAD(P)H-dependent enzymes.

7. Machine learning-assisted directed protein evolution with combinatorial libraries.

8. Development of a cancer-marker activated enzymatic switch from the herpes simplex virus thymidine kinase.

9. Tolerance of a Knotted Near-Infrared Fluorescent Protein to Random Circular Permutation.

10. The Structure of a Thermophilic Kinase Shapes Fitness upon Random Circular Permutation.