(Q38104437)

28 August 2017

title

Computational design gains momentum in enzyme catalysis engineering (English)

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28 August 2017

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Hein J Wijma

1

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28 August 2017

Dick B Janssen

series ordinal

2

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28 August 2017

language of work or name

English

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publication date

3 June 2013

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28 August 2017

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28 August 2017

volume

280

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28 August 2017

issue

13

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28 August 2017

page(s)

2948-2960

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Industrial biocatalysis today and tomorrow

28 August 2017

cites work

1 reference

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Beyond directed evolution—semi-rational protein engineering and design

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Kemp elimination catalysts by computational enzyme design

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Iterative approach to computational enzyme design

21 January 2018

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De novo computational design of retro-aldol enzymes

21 January 2018

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Robust design and optimization of retroaldol enzymes.

21 January 2018

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Computational Design of Catalytic Dyads and Oxyanion Holes for Ester Hydrolysis

21 January 2018

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De novo enzyme design using Rosetta3

21 January 2018

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Increased Diels-Alderase activity through backbone remodeling guided by Foldit players

21 January 2018

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Alteration of enzyme specificity by computational loop remodeling and design

21 January 2018

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Optimization of the In-Silico-Designed Kemp Eliminase KE70 by Computational Design and Directed Evolution

21 January 2018

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Design and evolution of new catalytic activity with an existing protein scaffold

21 January 2018

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A Simple Statistical Parameter for Use in Evaluation and Validation of High Throughput Screening Assays

21 January 2018

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Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers

21 January 2018

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Computational protein design promises to revolutionize protein engineering

21 January 2018

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Computational tools for designing and engineering biocatalysts

21 January 2018

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Computational design of affinity and specificity at protein-protein interfaces

21 January 2018

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Computational design of protein-ligand interfaces: potential in therapeutic development

21 January 2018

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Macromolecular modeling with rosetta

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Designing ensembles in conformational and sequence space to characterize and engineer proteins

21 January 2018

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Potential energy functions for protein design.

21 January 2018

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Electrostatics in computational protein design

21 January 2018

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Comprehensive computational design of mCreI homing endonuclease cleavage specificity for genome engineering

21 January 2018

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ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules

21 January 2018

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Conformational diversity and computational enzyme design

21 January 2018

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Progress in computational protein design

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12324

Computational structure-based redesign of enzyme activity

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12324

Computer design of obligate heterodimer meganucleases allows efficient cutting of custom DNA sequences

21 January 2018

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Bayesian statistical analysis of protein side-chain rotamer preferences

21 January 2018

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Using quantum mechanics to improve estimates of amino acid side chain rotamer energies

21 January 2018

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Conformer generation with OMEGA: algorithm and validation using high quality structures from the Protein Databank and Cambridge Structural Database

21 January 2018

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The Dynameomics rotamer library: amino acid side chain conformations and dynamics from comprehensive molecular dynamics simulations in water

21 January 2018

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Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction

21 January 2018

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GRID: a high-resolution protein structure refinement algorithm

21 January 2018

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RosettaLigand docking with full ligand and receptor flexibility.

21 January 2018

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Algorithm for backrub motions in protein design

21 January 2018

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Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design

21 January 2018

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Increasing Sequence Diversity with Flexible Backbone Protein Design: The Complete Redesign of a Protein Hydrophobic Core

21 January 2018

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Assessment of flexible backbone protein design methods for sequence library prediction in the therapeutic antibody Herceptin-HER2 interface

21 January 2018

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Biochemistry. Loop grafting and the origins of enzyme species.

21 January 2018

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RosettaRemodel: a generalized framework for flexible backbone protein design.

21 January 2018

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Computational design of enone-binding proteins with catalytic activity for the Morita-Baylis-Hillman reaction

21 January 2018

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Role of conformational sampling in computing mutation-induced changes in protein structure and stability

21 January 2018

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Computational protein design with explicit consideration of surface hydrophobic patches

21 January 2018

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Structure-guided forcefield optimization

21 January 2018

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New algorithms and an in silico benchmark for computational enzyme design

21 January 2018

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Design of protein-ligand binding based on the molecular-mechanics energy model

21 January 2018

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Origins of catalysis by computationally designed retroaldolase enzymes

21 January 2018

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Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design

21 January 2018

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Dramatic performance enhancements for the FASTER optimization algorithm

21 January 2018

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Dead-end elimination with perturbations (DEEPer): a provable protein design algorithm with continuous sidechain and backbone flexibility

21 January 2018

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The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles

21 January 2018

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A new generation of crystallographic validation tools for the protein data bank

21 January 2018

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MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

21 January 2018

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A computational methodology to screen activities of enzyme variants

21 January 2018

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Toward accurate screening in computer-aided enzyme design

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12324

Taking Ockham's razor to enzyme dynamics and catalysis

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12324

A hierarchy of timescales in protein dynamics is linked to enzyme catalysis

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12324

Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12324

Good vibrations in enzyme-catalysed reactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Evaluation and ranking of enzyme designs

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Most efficient cocaine hydrolase designed by virtual screening of transition states

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Computational redesign of human butyrylcholinesterase for anticocaine medication

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Free Energy Perturbation Simulation on Transition States and High-Activity Mutants of Human Butyrylcholinesterase for (−)-Cocaine Hydrolysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Computational design of an α-gliadin peptidase

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Design and directed evolution of a dideoxy purine nucleoside phosphorylase

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Computational design of orthogonal nucleoside kinases

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Computational redesign of endonuclease DNA binding and cleavage specificity

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Exploitation of binding energy for catalysis and design

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Engineering of large numbers of highly specific homing endonucleases that induce recombination on novel DNA targets

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Design, activity, and structure of a highly specific artificial endonuclease

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

A synthetic homing endonuclease-based gene drive system in the human malaria mosquito

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Design of a switchable eliminase

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Construction of a catalytically active iron superoxide dismutase by rational protein design

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Enzyme-like proteins by computational design

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Using multi-objective computational design to extend protein promiscuity.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Quantum mechanical design of enzyme active sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

The moderately efficient enzyme: evolutionary and physicochemical trends shaping enzyme parameters

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Off-the-shelf proteins that rival tailor-made antibodies as catalysts.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Engineering enzyme specificity using computational design of a defined-sequence library

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Modification of galactose oxidase to introduce glucose 6-oxidase activity

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Comparison of random mutagenesis and semi-rational designed libraries for improved cytochrome P450 BM3-catalyzed hydroxylation of small alkanes

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Evolutionary history of a specialized p450 propane monooxygenase

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

The influence of protein dynamics on the success of computational enzyme design

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Structural Analyses of Covalent Enzyme–Substrate Analog Complexes Reveal Strengths and Limitations of De Novo Enzyme Design

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Computational design of ligand binding is not a solved problem

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Computational design of an endo-1,4- -xylanase ligand binding site

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Key protein-design papers challenged.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Binding pocket optimization by computational protein design

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Stability effects of mutations and protein evolvability

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Relative tolerance of mesostable and thermostable protein homologs to extensive mutation

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Protein stability promotes evolvability

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Automated selection of stabilizing mutations in designed and natural proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Crystal structure of diisopropylfluorophosphatase from Loligo vulgaris

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

Evolutionary optimization of computationally designed enzymes: Kemp eliminases of the KE07 series

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

The dead-end elimination theorem and its use in protein side-chain positioning

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12324

21 January 2018

Identifiers

DOI

10.1111/FEBS.12324

1 reference

release_ozdjbbherzhgbmazbemaa75bgu

28 August 2017

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/ozdjbbherzhgbmazbemaa75bgu

mapped directly with Wikidata item

24 November 2022

based on heuristic

1 reference