Journal ArticleDOI
Complete inversion of enantioselectivity towards acetylated tertiary alcohols by a double mutant of a Bacillus subtilis esterase.
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This article is published in Angewandte Chemie.The article was published on 2008-02-08. It has received 141 citations till now. The article focuses on the topics: Bacillus subtilis & Esterase.read more
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Laboratory Evolution of Stereoselective Enzymes: A Prolific Source of Catalysts for Asymmetric Reactions
TL;DR: Emphasis is placed on the development of methods to make laboratory evolution faster and more efficient, thus providing chemists and biotechnologists with a rich and non-ending source of robust and selective catalysts for a variety of useful applications.
Journal ArticleDOI
Addressing the numbers problem in directed evolution
TL;DR: It is shown that the choice of the amino acid (aa) alphabet, as specified by the utilized codon degeneracy, provides the experimenter with a powerful tool in designing “smarter” randomized libraries that require considerably less screening effort.
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Computational enzyme design.
TL;DR: Computational "inside-out" design can lead to the production of catalytically active and selective proteins, but their kinetic performances fall short of natural enzymes when combined with directed evolution, molecular dynamics simulations, and crowd-sourced structure-prediction approaches.
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Directed enzyme evolution: climbing fitness peaks one amino acid at a time
TL;DR: Directed evolution can generate a remarkable range of new enzyme properties and activities on new substrates by improving variants with broadened specificities or by step-wise evolution through a sequence of more and more challenging substrates.
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Rational assignment of key motifs for function guides in silico enzyme identification
TL;DR: This work has developed an in silico strategy for a sequence-based prediction of substrate specificity and enantiopreference and discovered 17 (R)-selective amine transaminases, which catalyzed the synthesis of several (R-amines) with excellent optical purity up to >99% enantiomeric excess.
References
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Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
Garrett M. Morris,David S. Goodsell,Robert Scott Halliday,Ruth Huey,William E. Hart,Richard K. Belew,Arthur J. Olson +6 more
TL;DR: It is shown that both the traditional and Lamarckian genetic algorithms can handle ligands with more degrees of freedom than the simulated annealing method used in earlier versions of AUTODOCK, and that the Lamarckia genetic algorithm is the most efficient, reliable, and successful of the three.
Journal ArticleDOI
How Well Does a Restrained Electrostatic Potential (RESP) Model Perform in Calculating Conformational Energies of Organic and Biological Molecules
TL;DR: In this paper, the authors present conformational energies for a molecular mechanical model (Parm99) developed for organic and biological molecules using the restrained electrostatic potential (RESP) approach to derive the partial charges.
Journal Article
Python: a programming language for software integration and development.
TL;DR: In the laboratory, the laboratory investigates several areas, including protein-ligand docking, protein-protein docking, and complex molecular assemblies, as well as developing a number of computational tools such as molecular surfaces, phenomenological potentials, various docking and visualization programs which are used in conjunction with programs developed by others.
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Making optimal use of empirical energy functions: Force-field parameterization in crystal space
TL;DR: A new force field called YAMBER (Yet Another Model Building and Energy Refinement force field), which is shown to do significantly less damage to X‐ray structures, often move homology models in the right direction, and occasionally make them look like experimental structures.
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Improved biocatalysts by directed evolution and rational protein design.
Uwe T. Bornscheuer,Martina Pohl +1 more
TL;DR: The efficient application of biocatalysts requires the availability of suitable enzymes with high activity and stability under process conditions, desired substrate selectivity and high enantioselectivity, which often need to be optimized to fulfill these requirements.