Cheminformatic quantum mechanical enzyme model design: A catechol-O-methyltransferase case study

Single-Point Hessian Calculations for Improved Vibrational Frequencies and Rigid-Rotor-Harmonic-Oscillator Thermodynamics

(2021) Sebastian Spicher et al.   Journal of Chemical Theory and Computation

Using Atomic Confining Potentials for Geometry Optimization and Vibrational Frequency Calculations in Quantum-Chemical Models of Enzyme Active Sites

(2020) Saswata Dasgupta et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Examining the Origin of Catalytic Power of Catechol O-Methyltransferase

(2019) Xi Chen et al.   ACS Catalysis

A novel mechanism of heme degradation to biliverdin studied by QM/MM and QM calculations

(2018) Fatemeh Sadat Alavi et al.   DALTON TRANSACTIONS

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

Yoink: An interaction-based partitioning API

(2018) Min Zheng et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Catalytic Reaction Mechanism in Native and Mutant Catechol-O-methyltransferase from the Adaptive String Method and Mean Reaction Force Analysis

(2018) David Adrian Saez et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Large-scale QM/MM free energy simulations of enzyme catalysis reveal the influence of charge transfer

(2018) Heather J. Kulik   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Systematic Quantum Mechanical Region Determination in QM/MM Simulation

(2017) Maria Karelina et al.   Journal of Chemical Theory and Computation

Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures

(2017) Harry C Jubb et al.   JOURNAL OF MOLECULAR BIOLOGY

Quantified electrostatic preorganization in enzymes using the geometry of the electron charge density

(2017) Amanda Morgenstern et al.   Chemical Science

Protein environmental effects on iron-sulfur clusters: A set of rules for constructing computational models for inner and outer coordination spheres

(2016) Travis V. Harris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

How Large Should the QM Region Be in QM/MM Calculations? The Case of Catechol O-Methyltransferase

(2016) Heather J. Kulik et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Exploring the Dependence of QM/MM Calculations of Enzyme Catalysis on the Size of the QM Region

(2016) Garima Jindal et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Ab initio study of electronic interaction energies and desolvation energies for dopaminergic ligands in the catechol- O -methyltransferase active site

(2016) A. Katherine Hatstat et al.   Computational and Theoretical Chemistry

Computational Investigation of the Interplay of Substrate Positioning and Reactivity in Catechol O-Methyltransferase

(2016) Niladri Patra et al.   PLoS One

Convergence of Atomic Charges with the Size of the Enzymatic Environment

(2015) Danny E. P. Vanpoucke et al.   Journal of Chemical Information and Modeling

Simulation of the isotropic EXAFS spectra for the S2and S3structures of the oxygen evolving complex in photosystem II

(2015) Xichen Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accessory NUMM (NDUFS6) subunit harbors a Zn-binding site and is essential for biogenesis of mitochondrial complex I

(2015) Katarzyna Kmita et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Methyltransferases do not work by compression, cratic, or desolvation effects, but by electrostatic preorganization

(2015) Jeronimo Lameira et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The construction of an amino acid network for understanding protein structure and function

(2014) Wenying Yan et al.   AMINO ACIDS

Challenges within the Linear Response Approximation When Studying Enzyme Catalysis and Effects of Mutations

(2014) Avital Sharir-Ivry et al.   Journal of Chemical Theory and Computation

Linking Electrostatic Effects and Protein Motions in Enzymatic Catalysis. A Theoretical Analysis of Catechol O-Methyltransferase

(2014) Rafael García-Meseguer et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Computational Enzyme Design

(2013) Gert Kiss et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

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

Protein Contact Networks: An Emerging Paradigm in Chemistry

(2012) L. Di Paola et al.   CHEMICAL REVIEWS

A practical guide to modelling enzyme-catalysed reactions

(2012) Richard Lonsdale et al.   CHEMICAL SOCIETY REVIEWS

Accurate Reaction Energies in Proteins Obtained by Combining QM/MM and Large QM Calculations

(2012) LiHong Hu et al.   Journal of Chemical Theory and Computation

On the Convergence of QM/MM Energies

(2011) LiHong Hu et al.   Journal of Chemical Theory and Computation

Effect of the damping function in dispersion corrected density functional theory

(2011) Stefan Grimme et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Enzymatic Methyl Transfer: Role of an Active Site Residue in Generating Active Site Compaction That Correlates with Catalytic Efficiency

(2011) Jianyu Zhang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Analyzing and visualizing residue networks of protein structures

(2011) Nadezhda T. Doncheva et al.   TRENDS IN BIOCHEMICAL SCIENCES

Do Quantum Mechanical Energies Calculated for Small Models of Protein-Active Sites Converge?†

(2009) LiHong Hu et al.   JOURNAL OF PHYSICAL CHEMISTRY A

A Convergence Study of QM/MM Isomerization Energies with the Selected Size of the QM Region for Peptidic Systems†

(2009) Chris Vanessa Sumowski et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Evaluating Boundary Dependent Errors in QM/MM Simulations

(2009) Iván Solt et al.   JOURNAL OF PHYSICAL CHEMISTRY B

QM/MM simulations for methyl transfer in solution and catalysed by COMT: ensemble-averaging of kinetic isotope effects

(2008) Natalia Kanaan et al.   CHEMICAL COMMUNICATIONS

Crystal Structures of Human 108V and 108M Catechol O-Methyltransferase

(2008) K. Rutherford et al.   JOURNAL OF MOLECULAR BIOLOGY