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Advances in Molecular Dynamics Simulations and Enhanced Sampling Methods for the Study of Protein Systems

International journal of molecular sciences, 2020-09, Vol.21 (17), p.6339

2020

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Exploring indole channeling in tryptophan synthase using steered molecular dynamics simulation

Chemical physics letters, 2019-11, Vol.734, p.136701, Article 136701

2019

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Importance of protein dynamics in the structure-based drug discovery of class A G protein-coupled receptors (GPCRs)

Current opinion in structural biology, 2019-04, Vol.55, p.147-153

2019

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Application of conventional molecular dynamics simulation in evaluating the stability of apomyoglobin in urea solution

Scientific reports, 2017-03, Vol.7 (1), p.44651-44651, Article 44651

2017

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Structural Characterization of Receptor-Receptor Interactions in the Allosteric Modulation of G Protein-Coupled Receptor (GPCR) Dimers

International journal of molecular sciences, 2021-03, Vol.22 (6), p.3241

2021

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Multiscale Molecular Modeling in G Protein-Coupled Receptor (GPCR)-Ligand Studies

Biomolecules (Basel, Switzerland), 2020-04, Vol.10 (4), p.631

2020

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Incorporating Polarizability of Backbone Hydrogen Bonds Improved Folding of Short α-Helical Peptides

Biophysical journal, 2019-12, Vol.117 (11), p.2079-2086

2019

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Improved thermostability of Thermomyces lanuginosus lipase by molecular dynamics simulation and in silico mutation prediction and its application in biodiesel production

Fuel (Guildford), 2022-11, Vol.327, p.125039, Article 125039

2022

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Enhancing methanol tolerance of Thermomyces lanuginosus lipase by rational design and biodiesel production through one-step feeding of methanol

Journal of cleaner production, 2024-04, Vol.450, p.141949, Article 141949

2024

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Understanding the basis of I50V-induced affinity decrease in HIV-1 protease via molecular dynamics simulations using polarized force field

Journal of computational chemistry, 2015-09, Vol.36 (25), p.1885-1892

2015

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Importance of polarization effect in the study of metalloproteins: Application of polarized protein specific charge scheme in predicting the reduction potential of azurin

Proteins, structure, function, and bioinformatics, 2014-09, Vol.82 (9), p.2209-2219

2014

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Ab initio folding of mixed-fold FSD-EY protein using formula-based polarizable hydrogen bond (PHB) charge model

Chemical physics letters, 2017-09, Vol.684, p.24-29

2017

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Importance of polarization effect in the study of metalloproteins: Application of polarized protein specific charge scheme in predicting the reduction potential of azurin: Polarization Effect and Metalloproteins

Proteins, structure, function, and bioinformatics, 2014-09, Vol.82 (9), p.2209-2219

2014

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Ab initio folding of extended α-helix: A theoretical study about the role of electrostatic polarization in the folding of helical structures

Proteins, structure, function, and bioinformatics, 2013-09, Vol.81 (9), p.1610-1620

2013

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Ab initio folding of extended [alpha]-helix: A theoretical study about the role of electrostatic polarization in the folding of helical structures

Proteins, structure, function, and bioinformatics, 2013-09, Vol.81 (9), p.1610

2013

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Solvent effect on the folding dynamics and structure of E6-associated protein characterized from ab initio protein folding simulations

The Journal of chemical physics, 2012-04, Vol.136 (13), p.135102-135102-6

2012

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Stability of the β-structure in prion protein: A molecular dynamics study based on polarized force field

Chemical physics letters, 2012-06, Vol.539-540, p.239-244

2012

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Replica exchange molecular dynamics simulation of structure variation from α/4β-fold to 3α-fold protein

Journal of molecular modeling, 2012-03, Vol.18 (3), p.1087-1095

2012

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Computational study of bindings of HK20 Fab and D5 Fab to HIV-1 gp41

Bioorganic & medicinal chemistry letters, 2012-02, Vol.22 (4), p.1695-1700

2012

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Importance of Structure and Dynamics in the Rational Drug Design of G Protein‐Coupled Receptor ( GPCR ) Modulators

GPCRs as Therapeutic Targets, 2022, p.424-457

2022

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Via hole modeling of PZT thin films for MMIC applications

2008 IEEE International RF and Microwave Conference, 2008, p.222-225

2008

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Effect of grounding arrangement on PZT thin film capacitor

2007 Asia-Pacific Conference on Applied Electromagnetics, 2007, p.1-4

2007

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Etching characteristics of PZT thin films and via hole patterning for MMIC capacitors

2007 Asia-Pacific Conference on Applied Electromagnetics, 2007, p.1-4

2007

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Advances in Molecular Dynamics Simulations and Enhanced Sampling Methods for the Study of Protein Systems

Exploring indole channeling in tryptophan synthase using steered molecular dynamics simulation

Importance of protein dynamics in the structure-based drug discovery of class A G protein-coupled receptors (GPCRs)

Application of conventional molecular dynamics simulation in evaluating the stability of apomyoglobin in urea solution

Structural Characterization of Receptor-Receptor Interactions in the Allosteric Modulation of G Protein-Coupled Receptor (GPCR) Dimers

Multiscale Molecular Modeling in G Protein-Coupled Receptor (GPCR)-Ligand Studies

Incorporating Polarizability of Backbone Hydrogen Bonds Improved Folding of Short α-Helical Peptides

Improved thermostability of Thermomyces lanuginosus lipase by molecular dynamics simulation and in silico mutation prediction and its application in biodiesel production

Enhancing methanol tolerance of Thermomyces lanuginosus lipase by rational design and biodiesel production through one-step feeding of methanol

Understanding the basis of I50V-induced affinity decrease in HIV-1 protease via molecular dynamics simulations using polarized force field

Importance of polarization effect in the study of metalloproteins: Application of polarized protein specific charge scheme in predicting the reduction potential of azurin

Ab initio folding of mixed-fold FSD-EY protein using formula-based polarizable hydrogen bond (PHB) charge model

Importance of polarization effect in the study of metalloproteins: Application of polarized protein specific charge scheme in predicting the reduction potential of azurin: Polarization Effect and Metalloproteins

Ab initio folding of extended α-helix: A theoretical study about the role of electrostatic polarization in the folding of helical structures

Ab initio folding of extended [alpha]-helix: A theoretical study about the role of electrostatic polarization in the folding of helical structures

Solvent effect on the folding dynamics and structure of E6-associated protein characterized from ab initio protein folding simulations

Stability of the β-structure in prion protein: A molecular dynamics study based on polarized force field

Replica exchange molecular dynamics simulation of structure variation from α/4β-fold to 3α-fold protein

Computational study of bindings of HK20 Fab and D5 Fab to HIV-1 gp41

Importance of Structure and Dynamics in the Rational Drug Design of G Protein‐Coupled Receptor ( GPCR ) Modulators

Via hole modeling of PZT thin films for MMIC applications

Effect of grounding arrangement on PZT thin film capacitor

Etching characteristics of PZT thin films and via hole patterning for MMIC capacitors

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