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Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites

Nucleic acids research, 2018-01, Vol.46 (D1), p.D618-D623

2018

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The Catalytic Mechanism of HIV‑1 Integrase for DNA 3′-End Processing Established by QM/MM Calculations

Journal of the American Chemical Society, 2012-08, Vol.134 (32), p.13436-13447

2012

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Benchmarking of DFT Functionals for the Hydrolysis of Phosphodiester Bonds

Journal of chemical theory and computation, 2010-08, Vol.6 (8), p.2281-2292

2010

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The Catalytic Mechanism of Protein Phosphatase 5 Established by DFT Calculations

Chemistry : a European journal, 2013-10, Vol.19 (42), p.14081-14089

2013

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A global analysis of function and conservation of catalytic residues in enzymes

The Journal of biological chemistry, 2020-01, Vol.295 (2), p.314-324

2020

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Using mechanism similarity to understand enzyme evolution

Biophysical reviews, 2022-12, Vol.14 (6), p.1273-1280

2022

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Synthesis and Hydrolytic Studies on the Air-Stable [(4-CN-PhO)(E)P(μ‑N t Bu)]2 (E = O, S, and Se) Cyclodiphosphazanes

Inorganic chemistry, 2015-07, Vol.54 (13), p.6423-6432

2015

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Improving the Biodesulfurization of Crude Oil and Derivatives: A QM/MM Investigation of the Catalytic Mechanism of NADH-FMN Oxidoreductase (DszD)

The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 2016-07, Vol.120 (27), p.5300-5306

2016

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Emerging concepts in pseudoenzyme classification, evolution, and signaling

Science signaling, 2019-08, Vol.12 (594)

2019

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Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms

Wiley interdisciplinary reviews. Computational molecular science, 2017-03, Vol.7 (2), p.n/a

2017

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Enzymatic Flexibility and Reaction Rate: A QM/MM Study of HIV‑1 Protease

ACS catalysis, 2015-09, Vol.5 (9), p.5617-5626

2015

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Benchmarking of density functionals for the kinetics and thermodynamics of the hydrolysis of glycosidic bonds catalyzed by glycosidases

International journal of quantum chemistry, 2017-09, Vol.117 (18), p.n/a

2017

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Unique Triphenylphosphonium Derivatives for Enhanced Mitochondrial Uptake and Photodynamic Therapy

Bioconjugate chemistry, 2017-02, Vol.28 (2), p.590-599

2017

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GRaSP: a graph-based residue neighborhood strategy to predict binding sites

Bioinformatics, 2020-12, Vol.36 (Supplement_2), p.i726-i734

2020

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cuRRBS: simple and robust evaluation of enzyme combinations for reduced representation approaches

Nucleic acids research, 2017-11, Vol.45 (20), p.11559-11569

2017

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Insight into Enzymatic Nitrile Reduction: QM/MM Study of the Catalytic Mechanism of QueF Nitrile Reductase

ACS catalysis, 2015-06, Vol.5 (6), p.3740-3751

2015

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Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for copper complexes

Journal of computational chemistry, 2013-09, Vol.34 (24), p.2079-2090

2013

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Conformational Variation in Enzyme Catalysis: A Structural Study on Catalytic Residues

Journal of molecular biology, 2022-04, Vol.434 (7), p.167517-167517, Article 167517

2022

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The 3D Modules of Enzyme Catalysis: Deconstructing Active Sites into Distinct Functional Entities

Journal of molecular biology, 2023-10, Vol.435 (20), p.168254-168254, Article 168254

2023

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EzMechanism: an automated tool to propose catalytic mechanisms of enzyme reactions

Nature methods, 2023-10, Vol.20 (10), p.1516-1522

2023

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Catalytic Mechanism of Retroviral Integrase for the Strand Transfer Reaction Explored by QM/MM Calculations

Journal of chemical theory and computation, 2014-12, Vol.10 (12), p.5458-5466

2014

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GRaSP-web: a machine learning strategy to predict binding sites based on residue neighborhood graphs

Nucleic acids research, 2022-07, Vol.50 (W1), p.W392-W397

2022

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Analyses of cobalt–ligand and potassium–ligand bond lengths in metalloproteins: trends and patterns

Journal of molecular modeling, 2014-06, Vol.20 (6), p.2271-2271, Article 2271

2014

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New insights in the catalytic mechanism of tyrosine ammonia-lyase given by QM/MM and QM cluster models

Archives of biochemistry and biophysics, 2015-09, Vol.582, p.107-115

2015

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Exploring Chemical Biosynthetic Design Space with Transform-MinER

ACS synthetic biology, 2019-11, Vol.8 (11), p.2494-2506

2019

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Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites

The Catalytic Mechanism of HIV‑1 Integrase for DNA 3′-End Processing Established by QM/MM Calculations

Benchmarking of DFT Functionals for the Hydrolysis of Phosphodiester Bonds

The Catalytic Mechanism of Protein Phosphatase 5 Established by DFT Calculations

A global analysis of function and conservation of catalytic residues in enzymes

Using mechanism similarity to understand enzyme evolution

Synthesis and Hydrolytic Studies on the Air-Stable [(4-CN-PhO)(E)P(μ‑N t Bu)]2 (E = O, S, and Se) Cyclodiphosphazanes

Improving the Biodesulfurization of Crude Oil and Derivatives: A QM/MM Investigation of the Catalytic Mechanism of NADH-FMN Oxidoreductase (DszD)

Emerging concepts in pseudoenzyme classification, evolution, and signaling

Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms

Enzymatic Flexibility and Reaction Rate: A QM/MM Study of HIV‑1 Protease

Benchmarking of density functionals for the kinetics and thermodynamics of the hydrolysis of glycosidic bonds catalyzed by glycosidases

Unique Triphenylphosphonium Derivatives for Enhanced Mitochondrial Uptake and Photodynamic Therapy

GRaSP: a graph-based residue neighborhood strategy to predict binding sites

cuRRBS: simple and robust evaluation of enzyme combinations for reduced representation approaches

Insight into Enzymatic Nitrile Reduction: QM/MM Study of the Catalytic Mechanism of QueF Nitrile Reductase

Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for copper complexes

Conformational Variation in Enzyme Catalysis: A Structural Study on Catalytic Residues

The 3D Modules of Enzyme Catalysis: Deconstructing Active Sites into Distinct Functional Entities

EzMechanism: an automated tool to propose catalytic mechanisms of enzyme reactions

Catalytic Mechanism of Retroviral Integrase for the Strand Transfer Reaction Explored by QM/MM Calculations

GRaSP-web: a machine learning strategy to predict binding sites based on residue neighborhood graphs

Analyses of cobalt–ligand and potassium–ligand bond lengths in metalloproteins: trends and patterns

New insights in the catalytic mechanism of tyrosine ammonia-lyase given by QM/MM and QM cluster models

Exploring Chemical Biosynthetic Design Space with Transform-MinER

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