Exploiting enzyme evolution for computational protein design.
Trends Biochem Sci. 2022.
PMID: 34544655
Review.
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Computational Advances in Protein Engineering and Enzyme Design.
J Phys Chem B. 2022.
PMID: 35387452
No abstract available.
Computational design of a protein-based enzyme inhibitor.
J Mol Biol. 2013.
PMID: 23827138
Free PMC article.
Search results
Page 1
Exploiting enzyme evolution for computational protein design.
Trends Biochem Sci. 2022 May;47(5):375-389. doi: 10.1016/j.tibs.2021.08.008. Epub 2021 Sep 17.
Trends Biochem Sci. 2022.
PMID: 34544655
Free article.
Review.
Recent years have seen an explosion of interest in understanding the physicochemical parameters that shape enzyme evolution, as well as substantial advances in computational enzyme design. This review discusses three areas where evolutionary information can b …
Recent years have seen an explosion of interest in understanding the physicochemical parameters that shape enzyme evolution, as well as subs …
Computational enzyme design.
Angew Chem Int Ed Engl. 2013 May 27;52(22):5700-25. doi: 10.1002/anie.201204077. Epub 2013 Mar 25.
Angew Chem Int Ed Engl. 2013.
PMID: 23526810
Review.
Data-driven computational protein design.
Curr Opin Struct Biol. 2021 Aug;69:63-69. doi: 10.1016/j.sbi.2021.03.009. Epub 2021 Apr 25.
Curr Opin Struct Biol. 2021.
PMID: 33910104
Free PMC article.
Review.
Computational protein design can generate proteins not found in nature that adopt desired structures and perform novel functions. ...We present recent creative uses of multiple-sequence alignments, protein structures, and high-throughput functional assays in …
Computational protein design can generate proteins not found in nature that adopt desired structures and perform novel …
Computational protein design repurposed to explore enzyme vitality and help predict antibiotic resistance.
Front Mol Biosci. 2023 Jan 9;9:905588. doi: 10.3389/fmolb.2022.905588. eCollection 2022.
Front Mol Biosci. 2023.
PMID: 36699702
Free PMC article.
The property that reflects this is the enzyme "vitality", defined here as the difference between the inhibitor and substrate binding free energies. To predict such mutations, we borrow methodology from computational protein design. We use a Monte Carlo explor …
The property that reflects this is the enzyme "vitality", defined here as the difference between the inhibitor and substrate binding free en …
Computational protein design: a review.
J Phys Condens Matter. 2017 Apr 12;29(14):143001. doi: 10.1088/1361-648X/aa5c76. Epub 2017 Jan 31.
J Phys Condens Matter. 2017.
PMID: 28140371
Review.
The scope of this review is to describe the state of the art in computational protein design methods and give the reader an outline of what developments could be expected in the near future....
The scope of this review is to describe the state of the art in computational protein design methods and give the reade …
Computational protein design.
Curr Opin Chem Biol. 2001 Dec;5(6):690-5. doi: 10.1016/s1367-5931(01)00267-8.
Curr Opin Chem Biol. 2001.
PMID: 11738180
Review.
The field of computational protein design is reaching its adolescence. Protein design algorithms have been applied to design or engineer proteins that fold, fold faster, catalyze, catalyze faster, signal, and adopt preferred conformational states. Further dev …
The field of computational protein design is reaching its adolescence. Protein design algorithms have been applied to d …
The Framework of Computational Protein Design.
Methods Mol Biol. 2017;1529:3-19. doi: 10.1007/978-1-4939-6637-0_1.
Methods Mol Biol. 2017.
PMID: 27914044
Review.
Computational protein design (CPD) has established itself as a leading field in basic and applied science with a strong coupling between the two. ...
Computational protein design (CPD) has established itself as a leading field in basic and applied science with a strong …
De novo design of luciferases using deep learning.
Nature. 2023 Feb;614(7949):774-780. doi: 10.1038/s41586-023-05696-3. Epub 2023 Feb 22.
Nature. 2023.
PMID: 36813896
Free PMC article.
The creation of highly active and specific biocatalysts from scratch with broad applications in biomedicine is a key milestone for computational enzyme design, and our approach should enable generation of a wide range of luciferases and other enzymes....
The creation of highly active and specific biocatalysts from scratch with broad applications in biomedicine is a key milestone for comput …
Computational protein design with backbone plasticity.
Biochem Soc Trans. 2016 Oct 15;44(5):1523-1529. doi: 10.1042/BST20160155. Epub 2016 Oct 19.
Biochem Soc Trans. 2016.
PMID: 27911735
Free PMC article.
Review.
The incorporation of backbone flexibility into protein design is a much more computationally challenging problem due to the greatly increased search space, but promises to remove the limitations of reusing natural protein scaffolds. In this review, we outline the principles of …
The incorporation of backbone flexibility into protein design is a much more computationally challenging problem due to the greatly increase …
Principles and Methods in Computational Membrane Protein Design.
J Mol Biol. 2021 Oct 1;433(20):167154. doi: 10.1016/j.jmb.2021.167154. Epub 2021 Jul 14.
J Mol Biol. 2021.
PMID: 34271008
Review.
After decades of progress in computational protein design, the design of proteins folding and functioning in lipid membranes appears today as the next frontier. ...
After decades of progress in computational protein design, the design of proteins folding and functioning in lipid memb …
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