Using High-Throughput Molecular Dynamics Simulation to Enhance the Computational Design of Kemp Elimination Enzymes
Published 2023 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Using High-Throughput Molecular Dynamics Simulation to Enhance the Computational Design of Kemp Elimination Enzymes
Authors
Keywords
-
Journal
Journal of Chemical Information and Modeling
Volume 63, Issue 4, Pages 1323-1337
Publisher
American Chemical Society (ACS)
Online
2023-02-14
DOI
10.1021/acs.jcim.3c00002
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- The stability and dynamics of computationally designed proteins
- (2022) Natali A Gonzalez et al. PROTEIN ENGINEERING DESIGN & SELECTION
- The road to fully programmable protein catalysis
- (2022) Sarah L. Lovelock et al. NATURE
- A preorganization oriented computational method for de novo design of Kemp elimination enzymes
- (2022) Shengyu Zhang et al. ENZYME AND MICROBIAL TECHNOLOGY
- Efficient Lewis acid catalysis of an abiological reaction in a de novo protein scaffold
- (2021) Sophie Basler et al. Nature Chemistry
- Computational design of penicillin acylase variants with improved kinetic selectivity for the enzymatic synthesis of cefazolin
- (2021) Pengyu Wang et al. BIOCHEMICAL ENGINEERING JOURNAL
- Computational Prediction of ω-Transaminase Specificity by a Combination of Docking and Molecular Dynamics Simulations
- (2021) Carlos Ramírez-Palacios et al. Journal of Chemical Information and Modeling
- Engineering an efficient and enantioselective enzyme for the Morita–Baylis–Hillman reaction
- (2021) Rebecca Crawshaw et al. Nature Chemistry
- Contribution of Oxyanion Stabilization to Kemp Eliminase Efficiency
- (2020) Hajo Kries et al. ACS Catalysis
- Combinatorial Approach for Exploring Conformational Space and Activation Barriers in Computer-Aided Enzyme Design
- (2020) Dibyendu Mondal et al. ACS Catalysis
- ProdaMatch: A fast and accurate active site matching algorithm for de novo enzyme design
- (2020) Shengyu Zhang et al. COMPUTERS & CHEMICAL ENGINEERING
- Ensemble-based enzyme design can recapitulate the effects of laboratory directed evolution in silico
- (2020) Aron Broom et al. Nature Communications
- The challenge of predicting distal active site mutations in computational enzyme design
- (2020) Sílvia Osuna Wiley Interdisciplinary Reviews-Computational Molecular Science
- How directed evolution reshapes the energy landscape in an enzyme to boost catalysis
- (2020) Renee Otten et al. SCIENCE
- Synthetic biology 2020–2030: six commercially-available products that are changing our world
- (2020) Christopher A. Voigt Nature Communications
- Emergence of a Negative Activation Heat Capacity during Evolution of a Designed Enzyme
- (2019) H. Adrian Bunzel et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Improving the Efficiency of Ligand-Binding Protein Design with Molecular Dynamics Simulations
- (2019) Emilia P. Barros et al. Journal of Chemical Theory and Computation
- From directed evolution to computational enzyme engineering—A review
- (2019) Ratul Chowdhury et al. AICHE JOURNAL
- The evolution of multiple active site configurations in a designed enzyme
- (2018) Nan-Sook Hong et al. Nature Communications
- PubChem 2019 update: improved access to chemical data
- (2018) Sunghwan Kim et al. NUCLEIC ACIDS RESEARCH
- Computational Optimization of Electric Fields for Improving Catalysis of a Designed Kemp Eliminase
- (2017) Valerie Vaissier et al. ACS Catalysis
- Exploring the Development of Ground-State Destabilization and Transition-State Stabilization in Two Directed Evolution Paths of Kemp Eliminases
- (2017) Garima Jindal et al. ACS Catalysis
- Role of Conformational Dynamics in the Evolution of Retro-Aldolase Activity
- (2017) Adrian Romero-Rivera et al. ACS Catalysis
- The role of protein dynamics in the evolution of new enzyme function
- (2016) Eleanor Campbell et al. Nature Chemical Biology
- Emergence of a catalytic tetrad during evolution of a highly active artificial aldolase
- (2016) Richard Obexer et al. Nature Chemistry
- CHARMM36m: an improved force field for folded and intrinsically disordered proteins
- (2016) Jing Huang et al. NATURE METHODS
- Use of an Improved Matching Algorithm to Select Scaffolds for Enzyme Design Based on a Complex Active Site Model
- (2016) Xiaoqiang Huang et al. PLoS One
- Enantioselective Enzymes by Computational Design and In Silico Screening
- (2015) Hein J. Wijma et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- Computational design of enzyme–ligand binding using a combined energy function and deterministic sequence optimization algorithm
- (2015) Ye Tian et al. JOURNAL OF MOLECULAR MODELING
- Computational enzyme design: Transitioning from catalytic proteins to enzymes
- (2014) Wai Shun Mak et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Catalytic efficiency of designed catalytic proteins
- (2014) Ivan V Korendovych et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Computationally Efficient and Accurate Enantioselectivity Modeling by Clusters of Molecular Dynamics Simulations
- (2014) Hein J. Wijma et al. Journal of Chemical Information and Modeling
- Impact of scaffold rigidity on the design and evolution of an artificial Diels-Alderase
- (2014) N. Preiswerk et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Computational Design of Enone-Binding Proteins with Catalytic Activity for the Morita–Baylis–Hillman Reaction
- (2013) Sinisa Bjelic et al. ACS Chemical Biology
- Computational Enzyme Design
- (2013) Gert Kiss et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- Precision is essential for efficient catalysis in an evolved Kemp eliminase
- (2013) Rebecca Blomberg et al. NATURE
- Evolution of a designed retro-aldolase leads to complete active site remodeling
- (2013) Lars Giger et al. Nature Chemical Biology
- Systematic optimization model and algorithm for binding sequence selection in computational enzyme design
- (2013) Xiaoqiang Huang et al. PROTEIN SCIENCE
- Improving the accuracy of protein stability predictions with multistate design using a variety of backbone ensembles
- (2013) James A. Davey et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges
- (2012) K. Vanommeslaeghe et al. Journal of Chemical Information and Modeling
- Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing
- (2012) K. Vanommeslaeghe et al. Journal of Chemical Information and Modeling
- Extension of the CHARMM general force field to sulfonyl-containing compounds and its utility in biomolecular simulations
- (2012) Wenbo Yu et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations
- (2012) R. Anandakrishnan et al. NUCLEIC ACIDS RESEARCH
- Iterative approach to computational enzyme design
- (2012) H. K. Privett et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59
- (2012) O. Khersonsky et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Robust design and optimization of retroaldol enzymes
- (2012) Eric A. Althoff et al. PROTEIN SCIENCE
- Optimization of the In-Silico-Designed Kemp Eliminase KE70 by Computational Design and Directed Evolution
- (2011) Olga Khersonsky et al. JOURNAL OF MOLECULAR BIOLOGY
- A matching algorithm for catalytic residue site selection in computational enzyme design
- (2011) Yulin Lei et al. PROTEIN SCIENCE
- Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase
- (2010) M. P. Frushicheva et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Evaluation and ranking of enzyme designs
- (2010) Gert Kiss et al. PROTEIN SCIENCE
- Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction
- (2010) J. B. Siegel et al. SCIENCE
- CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields
- (2009) K. Vanommeslaeghe et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Molecular simulation of multistate peptide dynamics: A comparison between microsecond timescale sampling and multiple shorter trajectories
- (2008) Luca Monticelli et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Kemp elimination catalysts by computational enzyme design
- (2008) Daniela Röthlisberger et al. NATURE
- De Novo Computational Design of Retro-Aldol Enzymes
- (2008) L. Jiang et al. SCIENCE
- How Protein Stability and New Functions Trade Off
- (2008) Nobuhiko Tokuriki et al. PLoS Computational Biology
Find the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
SearchAdd your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload Now