Harder, better, faster, stronger: Large-scale QM and QM/MM for predictive modeling in enzymes and proteins

Biomolecular QM/MM Simulations: What Are Some of the “Burning Issues”?

(2021) Qiang Cui et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Highly Efficient Resolution-of-Identity Density Functional Theory Calculations on Central and Graphics Processing Units

(2021) Jörg Kussmann et al.   Journal of Chemical Theory and Computation

Systematic Detection and Characterization of Hydrogen Bonding in Proteins via Local Vibrational Modes

(2021) Niraj Verma et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Converged Structural and Spectroscopic Properties for Refined QM/MM Models of Azurin

(2021) Christine E. Schulz et al.   INORGANIC CHEMISTRY

Automated Construction of Quantum–Classical Hybrid Models

(2021) Christoph Brunken et al.   Journal of Chemical Theory and Computation

Modeling of Peptides with Classical and Novel Machine Learning Force Fields: A Comparison

(2021) David Rosenberger et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Exploring the Minimum-Energy Pathways and Free-Energy Profiles of Enzymatic Reactions with QM/MM Calculations

(2021) Kiyoshi Yagi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Non-Covalent Interactions Atlas Benchmark Data Sets: Hydrogen Bonding

(2020) Jan Řezáč   Journal of Chemical Theory and Computation

Both Configuration and QM Region Size Matter: Zinc Stability in QM/MM Models of DNA Methyltransferase

(2020) Rimsha Mehmood et al.   Journal of Chemical Theory and Computation

Improved Basis-Set Incompleteness Potentials for Accurate DFT Calculations in Large Systems

(2020) Alberto Otero-de-la-Roza et al.   Journal of Chemical Theory and Computation

Quantum Chemical Calculation of Molecular and Periodic Peptide and Protein Structures

(2020) Sarah Schmitz et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Environmental Effects on Guanine-Thymine Mispair Tautomerization Explored with Quantum Mechanical/Molecular Mechanical Free Energy Simulations

(2020) Pengfei Li et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Rapid Detection of Strong Correlation with Machine Learning for Transition-Metal Complex High-Throughput Screening

(2020) Fang Liu et al.   Journal of Physical Chemistry Letters

Biochemical and crystallographic investigations into isonitrile formation by a non-heme iron-dependent oxidase/decarboxylase

(2020) Rohan Jonnalagadda et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Adaptive Partitioning QM/MM for Molecular Dynamics Simulations: 6. Proton Transport through a Biological Channel

(2019) Adam W. Duster et al.   Journal of Chemical Theory and Computation

PEPCONF, a diverse data set of peptide conformational energies

(2019) Viki Kumar Prasad et al.   Scientific Data

Machine Learning Identifies Chemical Characteristics That Promote Enzyme Catalysis

(2019) Brian M. Bonk et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Evaluating Unexpectedly Short Non-covalent Distances in X-ray Crystal Structures of Proteins with Electronic Structure Analysis

(2019) Helena W. Qi et al.   Journal of Chemical Information and Modeling

Quantitative analysis of QM/MM boundary artifacts and correction in adaptive QM/MM simulations

(2019) Hiroshi C Watanabe et al.   Journal of Chemical Theory and Computation

The Protein’s Role in Substrate Positioning and Reactivity for Biosynthetic Enzyme Complexes: The Case of SyrB2/SyrB1

(2019) Rimsha Mehmood et al.   ACS Catalysis

Quantum Mechanical Description of Electrostatics Provides a Unified Picture of Catalytic Action Across Methyltransferases

(2019) Zhongyue Yang et al.   Journal of Physical Chemistry Letters

Predicting the Strength of Stacking Interactions between Heterocycles and Aromatic Amino Acid Side Chains

(2019) Andrea N. Bootsma et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Quantifying Inter-Residue Contacts through Interaction Energies

(2019) Thomas J. Summers et al.   Journal of Chemical Information and Modeling

Tracking Proton Transfer through Titratable Amino Acid Side Chains in Adaptive QM/MM Simulations

(2019) Adam W. Duster et al.   Journal of Chemical Theory and Computation

Finding Reactive Configurations: A Machine Learning Approach for Estimating Energy Barriers Applied to Sirtuin 5

(2019) Beatriz von der Esch et al.   Journal of Chemical Theory and Computation

Machine learning for protein folding and dynamics

(2019) Frank Noé et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Local energy decomposition analysis of hydrogen-bonded dimers within a domain-based pair natural orbital coupled cluster study

(2018) Ahmet Altun et al.   Beilstein Journal of Organic Chemistry

Fixed-Charge Atomistic Force Fields for Molecular Dynamics Simulations in the Condensed Phase: An Overview

(2018) Sereina Riniker   Journal of Chemical Information and Modeling

Rapid Convergence of Energy and Free Energy Profiles with Quantum Mechanical Size in Quantum Mechanical–Molecular Mechanical Simulations of Proton Transfer in DNA

(2018) Susanta Das et al.   Journal of Chemical Theory and Computation

Large-Scale Functional Group Symmetry-Adapted Perturbation Theory on Graphical Processing Units

(2018) Robert M. Parrish et al.   Journal of Chemical Theory and Computation

Toward Accurate QM/MM Reaction Barriers with Large QM Regions Using Domain Based Pair Natural Orbital Coupled Cluster Theory

(2018) Giovanni Bistoni et al.   Journal of Chemical Theory and Computation

Yoink: An interaction-based partitioning API

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

Cation–π interactions in protein–ligand binding: theory and data-mining reveal different roles for lysine and arginine

(2018) Kiran Kumar et al.   Chemical Science

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

(2018) Heather J. Kulik   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

QM/MM Study of the Nitrogenase MoFe Protein Resting State: Broken-Symmetry States, Protonation States, and QM Region Convergence in the FeMoco Active Site

(2017) Bardi Benediktsson et al.   INORGANIC CHEMISTRY

Iron Hydroperoxide Intermediate in Superoxide Reductase: Protonation or Dissociation First? MM Dynamics and QM/MM Metadynamics Study

(2017) Rolf David et al.   Journal of Chemical Theory and Computation

Unifying Exchange Sensitivity in Transition-Metal Spin-State Ordering and Catalysis through Bond Valence Metrics

(2017) Terry Z. H. Gani et al.   Journal of Chemical Theory and Computation

Influence of Coupling and Embedding Schemes on QM Size Convergence in QM/MM Approaches for the Example of a Proton Transfer in DNA

(2017) Sven Roßbach et al.   Journal of Chemical Theory and Computation

How Many Conformations Need To Be Sampled To Obtain Converged QM/MM Energies? The Curse of Exponential Averaging

(2017) Ulf Ryde   Journal of Chemical Theory and Computation

Systematic Quantum Mechanical Region Determination in QM/MM Simulation

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

Description of non-covalent interactions in SCC-DFTB methods

(2017) Vijay Madhav Miriyala et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

(2017) Amanda Morgenstern et al.   Chemical Science

Automated Selection of Active Orbital Spaces

(2016) Christopher J. Stein et al.   Journal of Chemical Theory and Computation

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

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

(2016) Niladri Patra et al.   PLoS One

Density Functional Theory and Hydrogen Bonds: Are We There Yet?

(2015) A. Daniel Boese   CHEMPHYSCHEM

Converging nuclear magnetic shielding calculations with respect to basis and system size in protein systems

(2015) Joshua D. Hartman et al.   JOURNAL OF BIOMOLECULAR NMR

Convergence of Atomic Charges with the Size of the Enzymatic Environment

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

Quantum Chemistry for Solvated Molecules on Graphical Processing Units Using Polarizable Continuum Models

(2015) Fang Liu et al.   Journal of Chemical Theory and Computation

Heuristics-Guided Exploration of Reaction Mechanisms

(2015) Maike Bergeler et al.   Journal of Chemical Theory and Computation

Quantifying the π-Stacking Interactions in Nitroarene Binding Sites of Proteins

(2015) Yi An et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mediation of donor–acceptor distance in an enzymatic methyl transfer reaction

(2015) Jianyu Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ribose-Protonated DNA Base Excision Repair: A Combined Theoretical and Experimental Study

(2014) Keyarash Sadeghian et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

A Density-Based Adaptive Quantum Mechanical/Molecular Mechanical Method

(2014) Mark P. Waller et al.   CHEMPHYSCHEM

Quantum Mechanical Calculation of Noncovalent Interactions: A Large-Scale Evaluation of PMx, DFT, and SAPT Approaches

(2014) Amanda Li et al.   Journal of Chemical Theory and Computation

Effect of Protein Environment within Cytochrome P450cam Evaluated Using a Polarizable-Embedding QM/MM Method

(2014) Nandun M. Thellamurege et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Recent developments in QM/MM methods towards open-boundary multi-scale simulations

(2014) Soroosh Pezeshki et al.   MOLECULAR SIMULATION

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

Convergence of Electronic Structure with the Size of the QM Region: Example of QM/MM NMR Shieldings

(2012) Denis Flaig et al.   Journal of Chemical Theory and Computation

Ab Initio Quantum Chemistry for Protein Structures

(2012) Heather J. Kulik et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods

(2011) Jan Řezáč 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

Utility of the Hard/Soft Acid−Base Principle via the Fukui Function in Biological Systems

(2010) John Faver et al.   Journal of Chemical Theory and Computation

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