Computer-aided understanding and engineering of enzymatic selectivity
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Title
Computer-aided understanding and engineering of enzymatic selectivity
Authors
Keywords
Computational aid, Enzymatic selectivity, Asymmetric biosynthesis, Protein engineering, Molecular mechanism, Quantum mechanical calculation, Enzyme channel
Journal
BIOTECHNOLOGY ADVANCES
Volume -, Issue -, Pages 107793
Publisher
Elsevier BV
Online
2021-07-02
DOI
10.1016/j.biotechadv.2021.107793
References
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- (2021) Che Yang et al. Nature Chemical Biology
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- (2021) Christoph K. Winkler et al. ACS Central Science
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- (2021) Giulia Sormani et al. JOURNAL OF CHEMICAL PHYSICS
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- (2021) Carlos G. Acevedo-Rocha et al. Nature Communications
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- (2021) Wenlong Zheng et al. ACS Catalysis
- Advances in machine learning for directed evolution
- (2021) Bruce J Wittmann et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
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- (2021) Sérgio M Marques et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
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- (2020) HyunA Park et al. BIOTECHNOLOGY ADVANCES
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- (2020) Paulo R. M. Pereira et al. Journal of Chemical Information and Modeling
- P450-BM3-Catalyzed Sulfoxidation versus Hydroxylation: A Common or Two Different Catalytically Active Species?
- (2020) Jian-bo Wang et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Inverted Binding of Non-natural Substrates in Strictosidine Synthase Leads to a Switch of Stereochemical Outcome in Enzyme-Catalyzed Pictet–Spengler Reactions
- (2020) Elisabeth Eger et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Improved protein structure prediction using potentials from deep learning
- (2020) Andrew W. Senior et al. NATURE
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- (2020) Jianyi Yang et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Protein Engineering for Improving and Diversifying Natural Product Biosynthesis
- (2020) Chenyi Li et al. TRENDS IN BIOTECHNOLOGY
- Enzyme-mediated two-step regio- and stereoselective synthesis of potential rapid acting antidepressant (2S,6S)-hydroxynorketamine
- (2020) Ansgar Bokel et al. ACS Catalysis
- Engineering new catalytic activities in enzymes
- (2020) Kai Chen et al. Nature Catalysis
- Regio‐ and Stereoselective Steroid Hydroxylation at C7 by Cytochrome P450 Monooxygenase Mutants
- (2020) Aitao Li et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- Synthesizing Chiral Drug Intermediates by Biocatalysis
- (2020) Wei Jiang et al. APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY
- Advances in molecular simulations of protein mechanical properties and function
- (2020) Florian Franz et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Dynamics, a Powerful Component of Current and Future in Silico Approaches for Protein Design and Engineering
- (2020) Bartłomiej Surpeta et al. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
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- (2020) Rita P. Magalhães et al. ISRAEL JOURNAL OF CHEMISTRY
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- (2020) Karl-Heinz Engel JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
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- (2020) Noelia Ferruz et al. JOURNAL OF MOLECULAR BIOLOGY
- Biosynthesis of a New Benzazepine Alkaloid Nanangelenin A from Aspergillus nanangensis Involves an Unusual l-Kynurenine-Incorporating NRPS Catalyzing Regioselective Lactamization
- (2020) Hang Li et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Macromolecular modeling and design in Rosetta: recent methods and frameworks
- (2020) Julia Koehler Leman et al. NATURE METHODS
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- (2020) Zibo Chen et al. SCIENCE
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- (2020) Fabian Sesterhenn et al. SCIENCE
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- (2020) Xiang Sheng et al. ACS Catalysis
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- (2020) April M. Cooper et al. npj Computational Materials
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- Prediction of higher-selectivity catalysts by computer-driven workflow and machine learning
- (2019) Andrew F. Zahrt et al. SCIENCE
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- (2019) Atsushi Tamada Symmetry-Basel
- Computational Protocol to Understand P450 Mechanisms and Design of Efficient and Selective Biocatalysts
- (2019) Kersti Caddell Haatveit et al. Frontiers in Chemistry
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- (2019) Aurélien de la Lande et al. MOLECULES
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- (2019) Jan Stourac et al. NUCLEIC ACIDS RESEARCH
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- (2019) Zachary Wu et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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- (2019) Chao Guo et al. ACS Catalysis
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- (2019) Ferran Planas et al. ACS Catalysis
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- (2019) Siyao Qiu et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- Advances in Sustainable Catalysis: A Computational Perspective
- (2019) Matthew G. Quesne et al. Frontiers in Chemistry
- The Crucial Role of Methodology Development in Directed Evolution of Selective Enzymes
- (2019) Ge Qu et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- Concepts of Artificial Intelligence for Computer-Assisted Drug Discovery
- (2019) Xin Yang et al. CHEMICAL REVIEWS
- Origins of Enantiopreference of Mycobacterium smegmatis Acyl Transferase: A Computational Analysis
- (2019) Masoud Kazemi et al. CHEMISTRY-A EUROPEAN JOURNAL
- Finding multiple reaction pathways of ligand unbinding
- (2019) Jakub Rydzewski et al. JOURNAL OF CHEMICAL PHYSICS
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- (2019) Zhongyue Yang et al. Journal of Physical Chemistry Letters
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- (2019) Xiang Sheng et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Modular and tunable biological feedback control using a de novo protein switch
- (2019) Andrew H. Ng et al. NATURE
- De novo design of bioactive protein switches
- (2019) Robert A. Langan et al. NATURE
- Holistic prediction of enantioselectivity in asymmetric catalysis
- (2019) Jolene P. Reid et al. NATURE
- Machine-learning-guided directed evolution for protein engineering
- (2019) Kevin K. Yang et al. NATURE METHODS
- Building a global alliance of biofoundries
- (2019) Nathan Hillson et al. Nature Communications
- Peroxide-Driven Hydroxylation of Small Alkanes Catalyzed by an Artificial P450BM3 Peroxygenase System
- (2019) Jie Chen et al. ACS Catalysis
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- (2019) Jakub Rydzewski COMPUTER PHYSICS COMMUNICATIONS
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- (2019) Qibin Chen et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Towards the online computer-aided design of catalytic pockets
- (2019) Laura Falivene et al. Nature Chemistry
- Advances in protein structure prediction and design
- (2019) Brian Kuhlman et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- Biocatalysis as Useful Tool in Asymmetric Synthesis: An Assessment of Recently Granted Patents (2014–2019)
- (2019) Pablo Domínguez de María et al. Catalysts
- From directed evolution to computational enzyme engineering—A review
- (2019) Ratul Chowdhury et al. AICHE JOURNAL
- Tunnel engineering to accelerate product release for better biomass-degrading abilities in lignocellulolytic enzymes
- (2019) Zhenghui Lu et al. Biotechnology for Biofuels
- Towards functional de novo designed proteins
- (2019) William M Dawson et al. CURRENT OPINION IN CHEMICAL BIOLOGY
- Prediction of CYP450 Enzyme–Substrate Selectivity Based on the Network-Based Label Space Division Method
- (2019) Xiaoqi Shan et al. Journal of Chemical Information and Modeling
- A computational method for design of connected catalytic networks in proteins
- (2019) Brian D. Weitzner et al. PROTEIN SCIENCE
- Recent developments in deep learning applied to protein structure prediction
- (2019) Shaun M. Kandathil et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Deep learning extends de novo protein modelling coverage of genomes using iteratively predicted structural constraints
- (2019) Joe G. Greener et al. Nature Communications
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- (2019) Reuben B. Leveson-Gower et al. Nature Reviews Chemistry
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- (2019) Ian Dance CHEMBIOCHEM
- Rational Design of Dehydrogenase/Reductases Based on Comparative Structural Analysis of Prereaction-State and Free-State Simulations for Efficient Asymmetric Reduction of Bulky Aryl Ketones
- (2019) Bing-Mei Su et al. ACS Catalysis
- Mechanism of Biocatalytic Friedel–Crafts Acylation by Acyltransferase from Pseudomonas protegens
- (2019) Xiang Sheng et al. ACS Catalysis
- Machine Learning in Enzyme Engineering
- (2019) Stanislav Mazurenko et al. ACS Catalysis
- Molecular switch manipulating Prelog priority of an alcohol dehydrogenase toward bulky-bulky ketones
- (2019) Guochao Xu et al. Molecular Catalysis
- CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories
- (2018) Adam Jurcik et al. BIOINFORMATICS
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- (2018) Guangyue Li et al. BIOORGANIC & MEDICINAL CHEMISTRY
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- (2018) Yuxin Li et al. ChemCatChem
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- (2018) Anthony R. Rosales et al. CHEMICAL COMMUNICATIONS
- Recent developments in the application of P450 based biocatalysts
- (2018) Yifeng Wei et al. CURRENT OPINION IN CHEMICAL BIOLOGY
- Are natural proteins special? Can we do that?
- (2018) Michael H Hecht et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Multiscale modeling of enzymes: QM-cluster, QM/MM, and QM/MM/MD: A tutorial review
- (2018) Shideh Ahmadi et al. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
- Effect of Binding on Enantioselectivity of Epoxide Hydrolase
- (2018) Julian Zaugg et al. Journal of Chemical Information and Modeling
- The market of chiral drugs: Chiral switches versus de novo enantiomerically pure compounds
- (2018) Andrea Calcaterra et al. JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
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- (2018) Ruifeng Li et al. Nature Chemical Biology
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- (2018) Lenka Sumbalova et al. NUCLEIC ACIDS RESEARCH
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- (2018) Wen-Juan Wang et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
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- (2018) Gideon Lapidoth et al. Nature Communications
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- (2018) Stefan E. Payer et al. ACS Catalysis
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- (2018) Fei-Fei Chen et al. ACS Catalysis
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- (2018) Yao Nie et al. ACS Catalysis
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- (2018) Silvia Rinaldi et al. ACS Catalysis
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- (2018) Fengyu Qin et al. ACS Catalysis
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- (2018) Hui-Xia Qian et al. INORGANIC CHEMISTRY
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- (2018) Jieyu Zhou et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Molecular Dynamics Simulation for All
- (2018) Scott A. Hollingsworth et al. NEURON
- Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity
- (2018) David J. Huggins et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- Chemo- and Regioselective Dihydroxylation of Benzene to Hydroquinone Enabled by Engineered Cytochrome P450 Monooxygenase
- (2018) Hangyu Zhou et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- The state-of-the-art strategies of protein engineering for enzyme stabilization
- (2018) Qian Liu et al. BIOTECHNOLOGY ADVANCES
- Unlocked potential of dynamic elements in protein structures: channels and loops
- (2018) Nico Kreß et al. CURRENT OPINION IN CHEMICAL BIOLOGY
- Stereoselective catalysis controlled by a native leucine or variant isoleucine wing-gatekeeper in 2-haloacid dehalogenase
- (2018) Yanbin Feng et al. FEBS LETTERS
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- (2018) You Lu et al. Journal of Chemical Theory and Computation
- De novo design of a non-local β-sheet protein with high stability and accuracy
- (2018) Enrique Marcos et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Exploring the challenges of computational enzyme design by rebuilding the active site of a dehalogenase
- (2018) Garima Jindal et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- In Silico Based Engineering Approach to Improve Transaminases for the Conversion of Bulky Substrates
- (2018) Moritz Voss et al. ACS Catalysis
- A machine learning approach for reliable prediction of amino acid interactions and its application in the directed evolution of enantioselective enzymes
- (2018) Frédéric Cadet et al. Scientific Reports
- Molecular dynamics simulations of macromolecular crystals
- (2018) David S. Cerutti et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
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- (2018) H. C. Stephen Chan et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
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- (2018) Wen-Jie Wei et al. Frontiers in Chemistry
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- (2018) Raphael Frey et al. CURRENT OPINION IN BIOTECHNOLOGY
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- (2017) Juan Pablo Acevedo et al. ENZYME AND MICROBIAL TECHNOLOGY
- Quantum chemical study of mechanism and stereoselectivity of secondary alcohol dehydrogenase
- (2017) Sara Moa et al. JOURNAL OF INORGANIC BIOCHEMISTRY
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- (2017) Gabriele Cruciani et al. JOURNAL OF MEDICINAL CHEMISTRY
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- Chiral Thioureas Promote Enantioselective Pictet–Spengler Cyclization by Stabilizing Every Intermediate and Transition State in the Carboxylic Acid-Catalyzed Reaction
- (2017) Rebekka S. Klausen et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
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- (2017) Zhoutong Sun et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Engineering protein stability with atomic precision in a monomeric miniprotein
- (2017) Emily G Baker et al. Nature Chemical Biology
- Ligand diffusion in proteins via enhanced sampling in molecular dynamics
- (2017) J. Rydzewski et al. Physics of Life Reviews
- MD simulations and QM/MM calculations show that single-site mutations of cytochrome P450BM3 alter the active site’s complexity and the chemoselectivity of oxidation without changing the active species
- (2017) Kshatresh Dutta Dubey et al. Chemical Science
- Theoretical Study of Enzyme Promiscuity: Mechanisms of Hydration and Carboxylation Activities of Phenolic Acid Decarboxylase
- (2017) Xiang Sheng et al. ACS Catalysis
- Reaction coordinates and transition states in enzymatic catalysis
- (2017) Kirill Zinovjev et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- Software update: the ORCA program system, version 4.0
- (2017) Frank Neese Wiley Interdisciplinary Reviews-Computational Molecular Science
- Engineering a Thermostable Keto Acid Decarboxylase Using Directed Evolution and Computationally Directed Protein Design
- (2017) Lemuel M. J. Soh et al. ACS Synthetic Biology
- CADEE: Computer-Aided Directed Evolution of Enzymes
- (2017) Beat Anton Amrein et al. IUCrJ
- Transition State Models for Understanding the Origin of Chiral Induction in Asymmetric Catalysis
- (2016) Raghavan B. Sunoj ACCOUNTS OF CHEMICAL RESEARCH
- Epoxide hydrolase-catalyzed enantioselective conversion of trans -stilbene oxide: Insights into the reaction mechanism from steady-state and pre-steady-state enzyme kinetics
- (2016) Alain Archelas et al. ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
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- (2016) Sebastian Kmiecik et al. CHEMICAL REVIEWS
- Transcriptional regulation of human and murine short-chain dehydrogenase/reductases (SDRs) – anin silicoapproach
- (2016) Bettina Ebert et al. DRUG METABOLISM REVIEWS
- Towards the computational design and engineering of enzyme enantioselectivity: A case study by a carbonyl reductase from Gluconobacter oxydans
- (2016) Jian Deng et al. JOURNAL OF BIOTECHNOLOGY
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- (2016) Rajeev Ramanan et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
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- (2016) Kshatresh Dutta Dubey et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- The coming of age of de novo protein design
- (2016) Po-Ssu Huang et al. NATURE
- Emergence of a catalytic tetrad during evolution of a highly active artificial aldolase
- (2016) Richard Obexer et al. Nature Chemistry
- Conformational diversity and enantioconvergence in potato epoxide hydrolase 1
- (2016) P. Bauer et al. ORGANIC & BIOMOLECULAR CHEMISTRY
- Biotechnology for Chemical Production: Challenges and Opportunities
- (2016) Mark J. Burk et al. TRENDS IN BIOTECHNOLOGY
- Quantum Chemical Modeling of Enantioconvergency in Soluble Epoxide Hydrolase
- (2016) Maria E. S. Lind et al. ACS Catalysis
- A Comprehensive Understanding of Enzymatic Catalysis by Hydroxynitrile Lyases with S Stereoselectivity from the α/β-Hydrolase Superfamily: Revised Role of the Active-Site Lysine and Kinetic Behavior of Substrate Delivery and Sequential Product Release
- (2016) Yuan Zhao et al. ACS Catalysis
- A switch in a substrate tunnel for directing regioselectivity of nitrile hydratases towards α,ω-dinitriles
- (2016) Zhongyi Cheng et al. Catalysis Science & Technology
- Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms
- (2016) Sérgio Filipe Sousa et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- Advances in Computational Prediction of Regioselective and Isoform-Specific Drug Metabolism Catalyzed by CYP450s.
- (2016) Vaibhav A. Dixit et al. ChemistrySelect
- Protein engineering by highly parallel screening of computationally designed variants
- (2016) M. G. F. Sun et al. Science Advances
- Reshaping an Enzyme Binding Pocket for Enhanced and Inverted Stereoselectivity: Use of Smallest Amino Acid Alphabets in Directed Evolution
- (2015) Zhoutong Sun et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- Expanding the Enzyme Universe: Accessing Non-Natural Reactions by Mechanism-Guided Directed Evolution
- (2015) Hans Renata et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- Redesigning alcohol dehydrogenases/reductases for more efficient biosynthesis of enantiopure isomers
- (2015) Rongzhen Zhang et al. BIOTECHNOLOGY ADVANCES
- Industrial applications of enzyme biocatalysis: Current status and future aspects
- (2015) Jung-Min Choi et al. BIOTECHNOLOGY ADVANCES
- CHEXVIS: a tool for molecular channel extraction and visualization
- (2015) Talha Bin Masood et al. BMC BIOINFORMATICS
- Quantum Mechanics/Molecular Mechanics Modeling of Enzymatic Processes: Caveats and Breakthroughs
- (2015) Matthew G. Quesne et al. CHEMISTRY-A EUROPEAN JOURNAL
- How quantum chemistry can solve fundamental problems in bioenergetics
- (2015) Margareta R. A. Blomberg INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
- DOCK 6: Impact of new features and current docking performance
- (2015) William J. Allen et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy
- (2015) Po-Ssu Huang et al. Nature Chemical Biology
- I-TASSER server: new development for protein structure and function predictions
- (2015) Jianyi Yang et al. NUCLEIC ACIDS RESEARCH
- Substrate tunnels in enzymes: Structure-function relationships and computational methodology
- (2015) Laura J. Kingsley et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Anatomy of enzyme channels
- (2014) Lukáš Pravda et al. BMC BIOINFORMATICS
- Hydrogen-Bonding-Driven Enantioselective Resolution against the Kazlauskas Rule To Afford γ-Amino Alcohols byCandida rugosaLipase
- (2014) Bora Min et al. CHEMBIOCHEM
- Unconserved substrate-binding sites direct the stereoselectivity of medium-chain alcohol dehydrogenase
- (2014) Shanshan Wang et al. CHEMICAL COMMUNICATIONS
- Quantum Chemical Studies of Mechanisms for Metalloenzymes
- (2014) Margareta R. A. Blomberg et al. CHEMICAL REVIEWS
- The role of reorganization energy in rational enzyme design
- (2014) Monika Fuxreiter et al. CURRENT OPINION IN CHEMICAL BIOLOGY
- P450BM3-Axial Mutations: A Gateway to Non-Natural Reactivity
- (2014) Todd K. Hyster et al. ISRAEL JOURNAL OF CHEMISTRY
- Substrate control in stereoselective lanthionine biosynthesis
- (2014) Weixin Tang et al. Nature Chemistry
- Computational design of water-soluble α-helical barrels
- (2014) Andrew R. Thomson et al. SCIENCE
- Theoretical Study of Reaction Mechanism and Stereoselectivity of Arylmalonate Decarboxylase
- (2014) Maria E. S. Lind et al. ACS Catalysis
- rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids
- (2014) Sergio Ruiz-Carmona et al. PLoS Computational Biology
- Quantum Chemistry as a Tool in Asymmetric Biocatalysis: Limonene Epoxide Hydrolase Test Case
- (2013) Maria E. S. Lind et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- Computational Enzyme Design
- (2013) Gert Kiss et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- De novo enzymes by computational design
- (2013) Hajo Kries et al. CURRENT OPINION IN CHEMICAL BIOLOGY
- Effect of Geometry Optimizations on QM-Cluster and QM/MM Studies of Reaction Energies in Proteins
- (2013) Sophie Sumner et al. Journal of Chemical Theory and Computation
- MOLE 2.0: advanced approach for analysis of biomacromolecular channels
- (2013) David Sehnal et al. Journal of Cheminformatics
- Determinants of Reactivity and Selectivity in Soluble Epoxide Hydrolase from Quantum Mechanics/Molecular Mechanics Modeling
- (2012) Richard Lonsdale et al. BIOCHEMISTRY
- Software tools for identification, visualization and analysis of protein tunnels and channels
- (2012) Jan Brezovsky et al. BIOTECHNOLOGY ADVANCES
- Epoxide Hydrolases and their Application in Organic Synthesis
- (2012) Michael Kotik et al. CURRENT ORGANIC CHEMISTRY
- An overview of the Amber biomolecular simulation package
- (2012) Romelia Salomon-Ferrer et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures
- (2012) Eva Chovancova et al. PLoS Computational Biology
- β2-adrenoceptor agonists: current and future direction
- (2011) Mario Cazzola et al. BRITISH JOURNAL OF PHARMACOLOGY
- P450BM3(CYP102A1): connecting the dots
- (2011) Christopher J. C. Whitehouse et al. CHEMICAL SOCIETY REVIEWS
- De Novo Enzyme Design Using Rosetta3
- (2011) Florian Richter et al. PLoS One
- Metadynamics
- (2011) Alessandro Barducci et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- The quantum chemical cluster approach for modeling enzyme reactions
- (2011) Per E.M. Siegbahn et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- Enantioselectivity of Haloalkane Dehalogenases and its Modulation by Surface Loop Engineering
- (2010) Zbynek Prokop et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- Folding and binding cascades: Dynamic landscapes and population shifts
- (2010) Sandeep Kumar et al. PROTEIN SCIENCE
- Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction
- (2010) J. B. Siegel et al. SCIENCE
- Exploring the Universe of Protein Structures beyond the Protein Data Bank
- (2010) Pilar Cossio et al. PLoS Computational Biology
- Hydrocarbon Hydroxylation by Cytochrome P450 Enzymes
- (2009) Paul R. Ortiz de Montellano CHEMICAL REVIEWS
- P450 Enzymes: Their Structure, Reactivity, and Selectivity—Modeled by QM/MM Calculations
- (2009) Sason Shaik et al. CHEMICAL REVIEWS
- AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
- (2009) Garrett M. Morris et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Probing the “Dark Matter” of Protein Fold Space
- (2009) William R. Taylor et al. STRUCTURE
- Changes of action potential and L-type calcium channel current of Sprague–Dawley rat ventricular myocytes by different amlodipine isomers
- (2008) Ru-xing Wang et al. CANADIAN JOURNAL OF PHYSIOLOGY AND PHARMACOLOGY
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