ReviewChemical communications (Cambridge, England)2016
Computational tools for the evaluation of laboratory-engineered biocatalysts.
Review in Chemical communications (Cambridge, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 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
38 citing papers in PubMed.
- Protein Catalysis Through Structural Dynamics: A Comprehensive Analysis of Energy Conversion in Enzymatic Systems and Its Computational Limitations.Pharmaceuticals (Basel, Switzerland) · 2025Review
- A Practical Guide to Computational Tools for Engineering Biocatalytic Properties.International journal of molecular sciences · 2025Review
- Ergothioneine biosynthesis: The present state and future prospect.Synthetic and systems biotechnology · 2025Review
- A Vision for the Future of Multiscale Modeling.ACS physical chemistry Au · 2024Review
- Review
- A high-performance electrochemical biosensor using an engineered urate oxidase.Chemical communications (Cambridge, England) · 2023Article
- AlphaFold2 and Deep Learning for Elucidating Enzyme Conformational Flexibility and Its Application for Design.JACS Au · 2023Review
- The Quantum Chemical Cluster Approach in Biocatalysis.Accounts of chemical research · 2023Review
- Data-driven strategies for the computational design of enzyme thermal stability: trends, perspectives, and prospects.Acta biochimica et biophysica Sinica · 2023Review
- Enzymatic Control over Reactive Intermediates Enables Direct Oxidation of Alkenes to Carbonyls by a P450 Iron-Oxo Species.Journal of the American Chemical Society · 2022Article
- Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2.Chemical reviews · 2022Review
- Experimental and computational studies of cellulases as bioethanol enzymes.Bioengineered · 2022Review
- Enhanced thermal and alkaline stability of L-lysine decarboxylase CadA by combining directed evolution and computation-guided virtual screening.Bioresources and bioprocessing · 2022Article
- Autonomous Reaction Network Exploration in Homogeneous and Heterogeneous Catalysis.Topics in catalysis · 2022Article
- Intelligent host engineering for metabolic flux optimisation in biotechnology.The Biochemical journal · 2021Review
- Recent advances in user-friendly computational tools to engineer protein function.Briefings in bioinformatics · 2021Review
- Pervasive cooperative mutational effects on multiple catalytic enzyme traits emerge via long-range conformational dynamics.Nature communications · 2021Article
- Machine Learning Enables Selection of Epistatic Enzyme Mutants for Stability Against Unfolding and Detrimental Aggregation.Chembiochem : a European journal of chemical biology · 2021Article
- Article
- Bioinformatic analysis of subfamily-specific regions in 3D-structures of homologs to study functional diversity and conformational plasticity in protein superfamilies.Computational and structural biotechnology journal · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Biocatalysis is based on the application of natural catalysts for new purposes, for which enzymes were not designed. Although the first examples of biocatalysis were reported more than a century ago, biocatalysis was revolutionized after the discovery of an in vitro version of Darwinian evolution called Directed Evolution (DE). Despite the recent advances in the field, major challenges remain to be addressed. Currently, the best experimental approach consists of creating multiple mutations simultaneously while limiting the choices using statistical methods. Still, tens of thousands of variants need to be tested experimentally, and little information is available on how these mutations lead to enhanced enzyme proficiency. This review aims to provide a brief description of the available computational techniques to unveil the molecular basis of improved catalysis achieved by DE. An overview of the strengths and weaknesses of current computational strategies is explored with some recent representative examples. The understanding of how this powerful technique is able to obtain highly active variants is important for the future development of more robust computational methods to predict amino-acid changes needed for activity.
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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.