Computational design gains momentum in enzyme catalysis engineering
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Title
Computational design gains momentum in enzyme catalysis engineering
Authors
Keywords
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Journal
FEBS Journal
Volume 280, Issue 13, Pages 2948-2960
Publisher
Wiley
Online
2013-05-06
DOI
10.1111/febs.12324
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Note: Only part of the references are listed.- Computational Design of Enone-Binding Proteins with Catalytic Activity for the Morita–Baylis–Hillman Reaction
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- (2012) Per-Olof Syrén et al. CHEMBIOCHEM
- Directed enzyme evolution: beyond the low-hanging fruit
- (2012) Moshe Goldsmith et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- GRID: A high-resolution protein structure refinement algorithm
- (2012) Mohsen Chitsaz et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers
- (2012) Michael D. Tyka et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Computational Design of Catalytic Dyads and Oxyanion Holes for Ester Hydrolysis
- (2012) Florian Richter et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
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- (2012) Sydney R. Gordon et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Engineering the third wave of biocatalysis
- (2012) U. T. Bornscheuer et al. NATURE
- Increased Diels-Alderase activity through backbone remodeling guided by Foldit players
- (2012) Christopher B Eiben et al. NATURE BIOTECHNOLOGY
- Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis
- (2012) Sagar D Khare et al. Nature Chemical Biology
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- (2012) Sam Hay et al. Nature Chemistry
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- (2012) David R. Glowacki et al. Nature Chemistry
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- (2012) Sarah Baxter et al. NUCLEIC ACIDS RESEARCH
- Binding Pocket Optimization by Computational Protein Design
- (2012) Christoph Malisi et al. PLoS One
- A Computational Methodology to Screen Activities of Enzyme Variants
- (2012) Martin R. Hediger et al. PLoS One
- Automated selection of stabilizing mutations in designed and natural proteins
- (2012) B. Borgo et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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- (2012) H. K. Privett et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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- (2011) I. V. Korendovych et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions
- (2011) A. J. Adamczyk et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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- (2011) Andrew Morin et al. TRENDS IN BIOTECHNOLOGY
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- (2009) Jiri Damborsky et al. CURRENT OPINION IN CHEMICAL BIOLOGY
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- (2009) John Karanicolas et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
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- Evolutionary Optimization of Computationally Designed Enzymes: Kemp Eliminases of the KE07 Series
- (2009) Olga Khersonsky et al. JOURNAL OF MOLECULAR BIOLOGY
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- (2009) Jory Z. Ruscio et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Exploitation of binding energy for catalysis and design
- (2009) Summer B. Thyme et al. NATURE
- Key protein-design papers challenged
- (2009) Erika Check Hayden NATURE
- Computational structure-based redesign of enzyme activity
- (2009) C.-Y. Chen et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Computational design of ligand binding is not a solved problem
- (2009) B. Schreier et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Alteration of enzyme specificity by computational loop remodeling and design
- (2009) P. M. Murphy et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Macromolecular Modeling with Rosetta
- (2008) Rhiju Das et al. Annual Review of Biochemistry
- Algorithm for backrub motions in protein design
- (2008) I. Georgiev et al. BIOINFORMATICS
- 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
- (2008) Ivelin Georgiev et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Evolutionary History of a Specialized P450 Propane Monooxygenase
- (2008) Rudi Fasan et al. JOURNAL OF MOLECULAR BIOLOGY
- Design of Protein–Ligand Binding Based on the Molecular-Mechanics Energy Model
- (2008) F. Edward Boas et al. JOURNAL OF MOLECULAR BIOLOGY
- Backrub-Like Backbone Simulation Recapitulates Natural Protein Conformational Variability and Improves Mutant Side-Chain Prediction
- (2008) Colin A. Smith et al. JOURNAL OF MOLECULAR BIOLOGY
- RosettaLigand Docking with Full Ligand and Receptor Flexibility
- (2008) Ian W. Davis et al. JOURNAL OF MOLECULAR BIOLOGY
- Quantum Mechanical Design of Enzyme Active Sites
- (2008) Xiyun Zhang et al. JOURNAL OF ORGANIC CHEMISTRY
- Most Efficient Cocaine Hydrolase Designed by Virtual Screening of Transition States
- (2008) Fang Zheng et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Catalytic Mechanism and Performance of Computationally Designed Enzymes for Kemp Elimination
- (2008) Anastassia N. Alexandrova et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases
- (2008) Pilar Redondo et al. NATURE
- Kemp elimination catalysts by computational enzyme design
- (2008) Daniela Röthlisberger et al. NATURE
- Computer design of obligate heterodimer meganucleases allows efficient cutting of custom DNA sequences
- (2008) Emmanuel Fajardo-Sanchez et al. NUCLEIC ACIDS RESEARCH
- De Novo Computational Design of Retro-Aldol Enzymes
- (2008) L. Jiang et al. SCIENCE
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