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Tyrosine absorption spectroscopy: Backbone protonation effects on the side chain electronic properties

Journal of computational chemistry, 2018-08, Vol.39 (22), p.1747-1756

2018

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Simulation of the Amide I Infrared Spectrum in Photoinduced Peptide Folding/Unfolding Transitions

The journal of physical chemistry. B, 2013-10, Vol.117 (41), p.12383-12390

2013

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Unambiguous Assignment of Reduction Potentials in Diheme Cytochromes

The journal of physical chemistry. B, 2014-07, Vol.118 (27), p.7554-7560

2014

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A quantitative connection of experimental and simulated folding landscapes by vibrational spectroscopyElectronic supplementary information (ESI) available: Temperature-dependent circular dichroism and FTIR, SVD analysis of the FTIR data, global fitting of thermal melts, Arrhenius plots of observed kinetics, expanded computational methods, the computational distribution of IR intensities, and complete tables of relaxation kinetics of 1619 cm−1, 1634 cm−1, 1661 cm−1 and 1680 cm−1. See DOI: 10.1039

2018-12

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Evidence for a high pKa of an aspartic acid residue in the active site of CALB by a fully atomistic multiscale approach

Journal of biomolecular structure & dynamics, 2023-07, Vol.41 (11), p.4949-4956

2023

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A Theoretical Reappraisal of Polylysine in the Investigation of Secondary Structure Sensitivity of Infrared Spectra

The journal of physical chemistry. B, 2012-03, Vol.116 (10), p.3353-3360

2012

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Alternative Fast and Slow Primary Charge‐Separation Pathways in Photosystem II

Angewandte Chemie, 2023-04, Vol.135 (16), p.n/a

2023

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Theoretical-computational modelling of infrared spectra in peptides and proteins: a new frontier for combined theoretical-experimental investigations

Current opinion in structural biology, 2010-04, Vol.20 (2), p.155-161

2010

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Common Folding Mechanism of a β-Hairpin Peptide via Non-native Turn Formation Revealed by Unbiased Molecular Dynamics Simulations

Journal of the American Chemical Society, 2009-12, Vol.131 (50), p.18147-18152

2009

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Monitoring the Folding Kinetics of a β‑Hairpin by Time-Resolved IR Spectroscopy in Silico

The journal of physical chemistry. B, 2015-04, Vol.119 (14), p.4849-4856

2015

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Photoexcitation and relaxation kinetics of molecular systems in solution: towards a complete in silico modelElectronic supplementary information (ESI) available. See DOI: 10.1039/c6cp06167b

2016-10

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Theoretical-computational modeling of photo-induced charge separation spectra and charge recombination kinetics in solutionElectronic supplementary information (ESI) available. See DOI: 10.1039/c4cp02422b

2014-09

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New Insight into the IR-Spectra/Structure Relationship in Amyloid Fibrils: A Theoretical Study on a Prion Peptide

Journal of the American Chemical Society, 2011-08, Vol.133 (30), p.11414-11417

2011

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Structural and dynamical properties of KTS-disintegrins: A comparison between Obtustatin and Lebestatin

Biopolymers, 2013-01, Vol.99 (1), p.47-54

2013

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Modeling quantum vibrational excitations in condensed-phase molecular systems

Theoretical chemistry accounts, 2011-05, Vol.129 (1), p.31-43

2011

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A few key residues determine the high redox potential shift in azurin mutantsElectronic supplementary information (ESI) available: Additional details of the quantum centre and additional analyses of the mutants' properties. See DOI: 10.1039/c5ob01819f

2015-11

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Mechanism of DNA Recognition by the Restriction Enzyme EcoRV

Journal of molecular biology, 2010-08, Vol.401 (3), p.415-432

2010

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On the structural affinity of macromolecules with different biological properties: Molecular dynamics simulations of a series of TEM-1 mutants

Biochemical and biophysical research communications, 2013-07, Vol.436 (4), p.666-671

2013

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Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

Journal of chemical information and modeling, 2020-12, Vol.60 (12)

2020

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Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

Journal of chemical information and modeling, 2020-12, Vol.60 (12)

2020

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Hit Expansion of a Noncovalent SARS-CoV‑2 Main Protease Inhibitor

ACS pharmacology & translational science, 2022-04, Vol.5 (4), p.255-265

2022

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Computational investigation of the electron transfer complex between neuroglobin and cytochrome c

Supramolecular chemistry, 2017-11, Vol.29 (11), p.846-852

2017

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Thermodynamic and kinetic characterization of a β-hairpin peptide in solution: An extended phase space sampling by molecular dynamics simulations in explicit water

Proteins, structure, function, and bioinformatics, 2005-05, Vol.59 (3), p.510-518

2005

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Analysis of Infrared Spectra of β-Hairpin Peptides As Derived from Molecular Dynamics Simulations

The journal of physical chemistry. B, 2011-10, Vol.115 (41), p.11872-11878

2011

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β-Hairpin conformation of fibrillogenic peptides: Structure and α-β transition mechanism revealed by molecular dynamics simulations

Proteins, structure, function, and bioinformatics, 2004-10, Vol.57 (1), p.198-204

2004

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Tyrosine absorption spectroscopy: Backbone protonation effects on the side chain electronic properties

Simulation of the Amide I Infrared Spectrum in Photoinduced Peptide Folding/Unfolding Transitions

Unambiguous Assignment of Reduction Potentials in Diheme Cytochromes

Evidence for a high pKa of an aspartic acid residue in the active site of CALB by a fully atomistic multiscale approach

A Theoretical Reappraisal of Polylysine in the Investigation of Secondary Structure Sensitivity of Infrared Spectra

Alternative Fast and Slow Primary Charge‐Separation Pathways in Photosystem II

Theoretical-computational modelling of infrared spectra in peptides and proteins: a new frontier for combined theoretical-experimental investigations

Common Folding Mechanism of a β-Hairpin Peptide via Non-native Turn Formation Revealed by Unbiased Molecular Dynamics Simulations

Monitoring the Folding Kinetics of a β‑Hairpin by Time-Resolved IR Spectroscopy in Silico

Photoexcitation and relaxation kinetics of molecular systems in solution: towards a complete in silico modelElectronic supplementary information (ESI) available. See DOI: 10.1039/c6cp06167b

Theoretical-computational modeling of photo-induced charge separation spectra and charge recombination kinetics in solutionElectronic supplementary information (ESI) available. See DOI: 10.1039/c4cp02422b

New Insight into the IR-Spectra/Structure Relationship in Amyloid Fibrils: A Theoretical Study on a Prion Peptide

Structural and dynamical properties of KTS-disintegrins: A comparison between Obtustatin and Lebestatin

Modeling quantum vibrational excitations in condensed-phase molecular systems

A few key residues determine the high redox potential shift in azurin mutantsElectronic supplementary information (ESI) available: Additional details of the quantum centre and additional analyses of the mutants' properties. See DOI: 10.1039/c5ob01819f

Mechanism of DNA Recognition by the Restriction Enzyme EcoRV

On the structural affinity of macromolecules with different biological properties: Molecular dynamics simulations of a series of TEM-1 mutants

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

Hit Expansion of a Noncovalent SARS-CoV‑2 Main Protease Inhibitor

Computational investigation of the electron transfer complex between neuroglobin and cytochrome c

Thermodynamic and kinetic characterization of a β-hairpin peptide in solution: An extended phase space sampling by molecular dynamics simulations in explicit water

Analysis of Infrared Spectra of β-Hairpin Peptides As Derived from Molecular Dynamics Simulations

β-Hairpin conformation of fibrillogenic peptides: Structure and α-β transition mechanism revealed by molecular dynamics simulations

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