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Multiscale molecular modelling: from electronic structure to dynamics of nanosystems and beyond

Physical chemistry chemical physics : PCCP, 2022-04, Vol.24 (16), p.951-981

Salahub, Dennis R

2022

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Potential bioactive glycosylated flavonoids as SARS-CoV-2 main protease inhibitors: A molecular docking and simulation studies

PloS one, 2020-10, Vol.15 (10), p.e0240653-e0240653

2020

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In silico identification of potential inhibitors of key SARS-CoV-2 3CL hydrolase (Mpro) via molecular docking, MMGBSA predictive binding energy calculations, and molecular dynamics simulation

PloS one, 2020-07, Vol.15 (7), p.e0235030-e0235030

2020

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Multiscale modeling of enzymes: QM‐cluster, QM/MM, and QM/MM/MD: A tutorial review

International journal of quantum chemistry, 2018-05, Vol.118 (9), p.n/a

2018

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Preface to the special collection in honor of Fernand Spiegelman

Theoretical chemistry accounts, 2021-10, Vol.140 (10), Article 133

2021

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Representation of Ion–Protein Interactions Using the Drude Polarizable Force-Field

The journal of physical chemistry. B, 2015-07, Vol.119 (29), p.9401-9416

2015

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Structure-thermodynamics-antioxidant activity relationships of selected natural phenolic acids and derivatives: an experimental and theoretical evaluation

PloS one, 2015-03, Vol.10 (3), p.e0121276-e0121276

2015

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Radical pairs may explain reactive oxygen species-mediated effects of hypomagnetic field on neurogenesis

PLoS computational biology, 2022-06, Vol.18 (6), p.e1010198

2022

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Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations

Journal of computational chemistry, 2007-01, Vol.28 (2), p.555-569

2007

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Simulating Electron Dynamics in Polarizable Environments

Journal of chemical theory and computation, 2017-09, Vol.13 (9), p.3985-4002

2017

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Molybdenum Carbide Nanocatalysts at Work in the in Situ Environment: A Density Functional Tight-Binding and Quantum Mechanical/Molecular Mechanical Study

Journal of the American Chemical Society, 2015-04, Vol.137 (12), p.4249-4259

2015

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Radical pairs may play a role in xenon-induced general anesthesia

Scientific reports, 2021-03, Vol.11 (1), p.6287-6287, Article 6287

2021

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Active-learning for global optimization of Ni-Ceria nanoparticles: The case of Ce 4-x Ni x O 8- x (x = 1, 2, 3)

Journal of computational chemistry, 2024-07, Vol.45 (19), p.1643

2024

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Reinforcement learning for in silico determination of adsorbate-substrate structures

Journal of computational chemistry, 2024-06, Vol.45 (15), p.1289-1302

2024

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Semiempirical Quantum Chemical PM6 Method Augmented by Dispersion and H-Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes

Journal of chemical theory and computation, 2009-07, Vol.5 (7), p.1749-1760

2009

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Mapping major SARS-CoV-2 drug targets and assessment of druggability using computational fragment screening: Identification of an allosteric small-molecule binding site on the Nsp13 helicase

PloS one, 2021-02, Vol.16 (2), p.e0246181

2021

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Constant pH molecular dynamics simulations of membrane proteins

Biophysical journal, 2023-02, Vol.122 (3), p.424a-424a

2023

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Active‐learning for global optimization of Ni‐Ceria nanoparticles: The case of Ce4−xNixO8−x (x=1, 2, 3)

Journal of computational chemistry, 2024-07, Vol.45 (19), p.1643-1656

2024

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A community-powered search of machine learning strategy space to find NMR property prediction models

PloS one, 2021-07, Vol.16 (7), p.e0253612-e0253612

2021

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Benchmarking polarizable and non-polarizable force fields for Ca2+–peptides against a comprehensive QM dataset

The Journal of chemical physics, 2020-10, Vol.153 (14), p.144102-144102

2020

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Selective ion binding and transport by membrane proteins – A computational perspective

Coordination chemistry reviews, 2017-08, Vol.345, p.108-136

2017

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Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review

Molecules (Basel, Switzerland), 2019-04, Vol.24 (9), p.1653

2019

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A quantum chemical approach representing a new perspective concerning agonist and antagonist drugs in the context of schizophrenia and Parkinson's disease

PloS one, 2019-12, Vol.14 (12), p.e0224691

2019

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A transformer-based model to predict peptide–HLA class I binding and optimize mutated peptides for vaccine design

Nature machine intelligence, 2022-03, Vol.4 (3), p.300-311

2022

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Heterogeneous reactions of SO2 on the hematite(0001) surface

The Journal of chemical physics, 2018-11, Vol.149 (19), p.194703-194703

2018

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Multiscale molecular modelling: from electronic structure to dynamics of nanosystems and beyond

Potential bioactive glycosylated flavonoids as SARS-CoV-2 main protease inhibitors: A molecular docking and simulation studies

In silico identification of potential inhibitors of key SARS-CoV-2 3CL hydrolase (Mpro) via molecular docking, MMGBSA predictive binding energy calculations, and molecular dynamics simulation

Multiscale modeling of enzymes: QM‐cluster, QM/MM, and QM/MM/MD: A tutorial review

Preface to the special collection in honor of Fernand Spiegelman

Representation of Ion–Protein Interactions Using the Drude Polarizable Force-Field

Structure-thermodynamics-antioxidant activity relationships of selected natural phenolic acids and derivatives: an experimental and theoretical evaluation

Radical pairs may explain reactive oxygen species-mediated effects of hypomagnetic field on neurogenesis

Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations

Simulating Electron Dynamics in Polarizable Environments

Molybdenum Carbide Nanocatalysts at Work in the in Situ Environment: A Density Functional Tight-Binding and Quantum Mechanical/Molecular Mechanical Study

Radical pairs may play a role in xenon-induced general anesthesia

Active-learning for global optimization of Ni-Ceria nanoparticles: The case of Ce 4-x Ni x O 8- x (x = 1, 2, 3)

Reinforcement learning for in silico determination of adsorbate-substrate structures

Semiempirical Quantum Chemical PM6 Method Augmented by Dispersion and H-Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes

Mapping major SARS-CoV-2 drug targets and assessment of druggability using computational fragment screening: Identification of an allosteric small-molecule binding site on the Nsp13 helicase

Constant pH molecular dynamics simulations of membrane proteins

Active‐learning for global optimization of Ni‐Ceria nanoparticles: The case of Ce4−xNixO8−x (x=1, 2, 3)

A community-powered search of machine learning strategy space to find NMR property prediction models

Benchmarking polarizable and non-polarizable force fields for Ca2+–peptides against a comprehensive QM dataset

Selective ion binding and transport by membrane proteins – A computational perspective

Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review

A quantum chemical approach representing a new perspective concerning agonist and antagonist drugs in the context of schizophrenia and Parkinson's disease

A transformer-based model to predict peptide–HLA class I binding and optimize mutated peptides for vaccine design

Heterogeneous reactions of SO2 on the hematite(0001) surface

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