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Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations

Nature communications, 2016-08, Vol.7 (1), p.12575-12575, Article 12575

2016

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FFParam: Standalone package for CHARMM additive and Drude polarizable force field parametrization of small molecules

Journal of computational chemistry, 2020-04, Vol.41 (9), p.958-970

2020

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Conformational Gating Dynamics in the GluCl Anion-Selective Chloride Channel

ACS chemical neuroscience, 2015-08, Vol.6 (8), p.1459-1467

2015

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Allosteric binding site in a Cys-loop receptor ligand-binding domain unveiled in the crystal structure of ELIC in complex with chlorpromazine

Proceedings of the National Academy of Sciences - PNAS, 2016-10, Vol.113 (43), p.E6696-E6703

2016

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Assessment of homology templates and an anesthetic binding site within the ?-aminobutyric acid receptor

Anesthesiology (Philadelphia), 2013-11, Vol.119 (5), p.1087

2013

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Simple Synthesis of a Heterocyclophane Exhibiting Anti‐c‐Met Activity by Acting as a Hatch Blocking Access to the Active Site

Chemistry : a European journal, 2021-01, Vol.27 (5), p.1648-1654

2021

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Exploring the Conformational Impact of Glycine Receptor TM1-2 Mutations Through Coarse-Grained Analysis and Atomistic Simulations

Frontiers in molecular biosciences, 2022-06, Vol.9, p.890851

2022

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Principal Components from Ligand-Gated Ion Channel Structures Enable Ensemble Studies of Microsecond-Scale Transitions

Biophysical journal, 2016-02, Vol.110 (3), p.454a-454a

2016

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Transmembrane Structural Determinants of Alcohol Binding and Modulation in a Model Ligand-Gated Ion Channel

Biophysical journal, 2017-02, Vol.112 (3), p.554a-554a

2017

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Functional characterization of neurotransmitter activation and modulation in a nematode model ligand‐gated ion channel

Journal of neurochemistry, 2016-07, Vol.138 (2), p.243-253

2016

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Stabilization of the GluCl Ligand-Gated Ion Channel in the Presence and Absence of Ivermectin

Biophysical journal, 2013-08, Vol.105 (3), p.640-647

2013

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Alcohol Modulation of a Eukaryotic Ligand-Gated Ion Channel of Known Structure

Biophysical journal, 2014, Vol.106 (2), p.545a-545a

2014

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Contribution of Structural Elements to Activation and Allosteric Modulation in an Anionic Ligand-Gated Ion Channel

Biophysical journal, 2014, Vol.106 (2), p.547a-547a

2014

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eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spaces

Bioinformatics, 2019-09, Vol.35 (18), p.3505-3507

2019

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Elucidating Complimentary Base Specificity of Thymine DNA Glycosylase via Potential of Mean Force Molecular Dynamics Simulations

Biophysical journal, 2019-02, Vol.116 (3), p.21-22a

2019

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Molecular Dynamics Simulation Study of DNA Mismatch Recognition by Complementary Strand Interactions in Thymine DNA Glycosylase

Biophysical journal, 2018-02, Vol.114 (3), p.84a-85a

2018

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Exploring the Gating Pathway in an Eukaryotic Ligand-Gated Ion Channel

Biophysical journal, 2015, Vol.108 (2), p.433a-433a

2015

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Study on the Mechanism of Anti C-Met Activity of Boc-Protected Amino Groups of Bithiazolophanes by using SILCS

Biophysical journal, 2019-02, Vol.116 (3), p.483a-483a

2019

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Cover Feature: Simple Synthesis of a Heterocyclophane Exhibiting Anti‐c‐Met Activity by Acting as a Hatch Blocking Access to the Active Site (Chem. Eur. J. 5/2021)

Chemistry : a European journal, 2021-01, Vol.27 (5), p.1479-1479

2021

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Revealing the Mechanism for Conformational Changes from Structurally Rich Ensembles

Biophysical journal, 2016-02, Vol.110 (3), p.54a-54a

2016

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Assessment of Homology Templates and an Anesthetic Binding Site within the γ-Aminobutyric Acid Receptor

Anesthesiology (Philadelphia), 2013-11, Vol.119 (5), p.1087-1095

2013

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Gating Ritual: Simulations of Gating in Glutamate-Gated Chloride Channel

Biophysical journal, 2015, Vol.108 (2), p.431a-431a

2015

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Improved Comparative Models of Human Gabaar Ligand-Gated Ion Channels Based on Structural Dynamics of GluCl

Biophysical journal, 2013, Vol.104 (2), p.638a-638a

2013

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Microsecond time-scale dynamics of the pentameric ligand-gated ion channels: a comparative study

European biophysics journal, 2015, Vol.44, p.S219

2015

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Abstract PO5-27-05: Computational design and validation of a novel peptide-drug conjugate for treatment of triple negative breast cancer

Cancer research (Chicago, Ill.), 2024-05, Vol.84 (9_Supplement), p.PO5-27-05-PO5-27-05

2024

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Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations

FFParam: Standalone package for CHARMM additive and Drude polarizable force field parametrization of small molecules

Conformational Gating Dynamics in the GluCl Anion-Selective Chloride Channel

Allosteric binding site in a Cys-loop receptor ligand-binding domain unveiled in the crystal structure of ELIC in complex with chlorpromazine

Assessment of homology templates and an anesthetic binding site within the ?-aminobutyric acid receptor

Simple Synthesis of a Heterocyclophane Exhibiting Anti‐c‐Met Activity by Acting as a Hatch Blocking Access to the Active Site

Exploring the Conformational Impact of Glycine Receptor TM1-2 Mutations Through Coarse-Grained Analysis and Atomistic Simulations

Principal Components from Ligand-Gated Ion Channel Structures Enable Ensemble Studies of Microsecond-Scale Transitions

Transmembrane Structural Determinants of Alcohol Binding and Modulation in a Model Ligand-Gated Ion Channel

Functional characterization of neurotransmitter activation and modulation in a nematode model ligand‐gated ion channel

Stabilization of the GluCl Ligand-Gated Ion Channel in the Presence and Absence of Ivermectin

Alcohol Modulation of a Eukaryotic Ligand-Gated Ion Channel of Known Structure

Contribution of Structural Elements to Activation and Allosteric Modulation in an Anionic Ligand-Gated Ion Channel

eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spaces

Elucidating Complimentary Base Specificity of Thymine DNA Glycosylase via Potential of Mean Force Molecular Dynamics Simulations

Molecular Dynamics Simulation Study of DNA Mismatch Recognition by Complementary Strand Interactions in Thymine DNA Glycosylase

Exploring the Gating Pathway in an Eukaryotic Ligand-Gated Ion Channel

Study on the Mechanism of Anti C-Met Activity of Boc-Protected Amino Groups of Bithiazolophanes by using SILCS

Cover Feature: Simple Synthesis of a Heterocyclophane Exhibiting Anti‐c‐Met Activity by Acting as a Hatch Blocking Access to the Active Site (Chem. Eur. J. 5/2021)

Revealing the Mechanism for Conformational Changes from Structurally Rich Ensembles

Assessment of Homology Templates and an Anesthetic Binding Site within the γ-Aminobutyric Acid Receptor

Gating Ritual: Simulations of Gating in Glutamate-Gated Chloride Channel

Improved Comparative Models of Human Gabaar Ligand-Gated Ion Channels Based on Structural Dynamics of GluCl

Microsecond time-scale dynamics of the pentameric ligand-gated ion channels: a comparative study

Abstract PO5-27-05: Computational design and validation of a novel peptide-drug conjugate for treatment of triple negative breast cancer

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