ReviewCurrent opinion in chemical biology2010
Conformational diversity and computational enzyme design.
Review in Current opinion in chemical biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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.
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.
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Who cites it
20 citing papers in PubMed.
- Dynamic-Structure Redesign of Calmodulin Reveals Mechanistic Constraints on Ryr2 Regulation.bioRxiv : the preprint server for biology · 2026Article
- Getting 'ϕψχal' with proteins: minimum message length inference of joint distributions of backbone and sidechain dihedral angles.Bioinformatics (Oxford, England) · 2023Article
- Thiazole-amino acids: influence of thiazole ring on conformational properties of amino acid residues.Amino acids · 2021Article
- Enhancing cellulosic ethanol production through coevolution of multiple enzymatic characteristics of β-glucosidase from Penicillium oxalicum 16.Applied microbiology and biotechnology · 2020Article
- Evolution of chalcone isomerase from a noncatalytic ancestor.Nature chemical biology · 2018Article
- Engineered control of enzyme structural dynamics and function.Protein science : a publication of the Protein Society · 2018Review
- Article
- Computational Redesign of Thioredoxin Is Hypersensitive toward Minor Conformational Changes in the Backbone Template.Journal of molecular biology · 2016Article
- Perspective: Defining and quantifying the role of dynamics in enzyme catalysis.The Journal of chemical physics · 2016Review
- Linking coupled motions and entropic effects to the catalytic activity of 2-deoxyribose-5-phosphate aldolase (DERA).Chemical science · 2016Article
- Computational study of a model system of enzyme-mediated [4+2] cycloaddition reaction.PloS one · 2015Article
- The effect of the hydrophobic environment on the retro-aldol reaction: comparison to a computationally-designed enzyme.Organic & biomolecular chemistry · 2013Article
- Conservation of flexible residue clusters among structural and functional enzyme homologues.The Journal of biological chemistry · 2012Article
- Computational protein engineering: bridging the gap between rational design and laboratory evolution.International journal of molecular sciences · 2012Review
- Computational design of a Diels-Alderase from a thermophilic esterase: the importance of dynamics.Journal of computer-aided molecular design · 2012Article
- Multistate approaches in computational protein design.Protein science : a publication of the Protein Society · 2012Review
- Article
- Computational Enzyme Design: Advances, hurdles and possible ways forward.Computational and structural biotechnology journal · 2012Review
- Enzyme informatics.Current topics in medicinal chemistry · 2012Review
- Challenges and advances in validating enzyme design proposals: the case of kemp eliminase catalysis.Biochemistry · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
Abstract
The application of computational protein design methods to the design of enzyme active sites offers potential routes to new catalysts and new reaction specificities. Computational design methods have typically treated the protein backbone as a rigid structure for the sake of computational tractability. However, this fixed-backbone approximation introduces its own special challenges for enzyme design and it contrasts with an emerging picture of natural enzymes as dynamic ensembles with multiple conformations and motions throughout a reaction cycle. This review considers the impact of conformational variation and dynamics on computational enzyme design and it highlights new approaches to addressing protein conformational diversity in enzyme design including recent advances in multi-state design, backbone flexibility, and computational library design.
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Registered trials
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