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Disordered linkers in multidomain allosteric proteins: Entropic effect to favor the open state or enhanced local concentration to favor the closed state?

Protein science, 2018-09, Vol.27 (9), p.1600-1610

2018

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MD simulations reveal alternate conformations of the oxyanion hole in the Zika virus NS2B/NS3 protease

Proteins, structure, function, and bioinformatics, 2020-02, Vol.88 (2), p.345-354

2020

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Identification of a conserved 8 aa insert in the PIP5K protein in the Saccharomycetaceae family of fungi and the molecular dynamics simulations and structural analysis to investigate its potential functional role

Proteins, structure, function, and bioinformatics, 2017-08, Vol.85 (8), p.1454-1467

2017

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Atomic-level characterization of protein–protein association

Proceedings of the National Academy of Sciences - PNAS, 2019-03, Vol.116 (10), p.4244-4249

2019

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Structural and Evolutionary Analysis Indicate That the SARS-CoV-2 Mpro Is a Challenging Target for Small-Molecule Inhibitor Design

International journal of molecular sciences, 2020-04, Vol.21 (9), p.3099

2020

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Deciphering the crucial molecular properties of a series of Benzothiazole Hydrazone inhibitors that targets anti-apoptotic Bcl-xL protein

Journal of biomolecular structure & dynamics, 2018-07, Vol.36 (10), p.2654-2667

2018

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Interaction of novel Aurora kinase inhibitor MK-0457 with human serum albumin: Insights into the dynamic behavior, binding mechanism, conformation and esterase activity of human serum albumin

Journal of pharmaceutical and biomedical analysis, 2020-01, Vol.178, p.112962-112962, Article 112962

2020

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Aβ Monomers Transiently Sample Oligomer and Fibril-Like Configurations: Ensemble Characterization Using a Combined MD/NMR Approach

Journal of molecular biology, 2013-09, Vol.425 (18), p.3338-3359

2013

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The interaction of Naphthol Yellow S (NYS) with pepsin: Insights from spectroscopic to molecular dynamics studies

International journal of biological macromolecules, 2020-12, Vol.165 (Pt B), p.1842-1851

2020

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Advances in computational methods for ligand binding kinetics

Trends in biochemical sciences (Amsterdam. Regular ed.), 2023-05, Vol.48 (5), p.437-449

2023

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Molecular dynamics simulations and drug discovery

BMC biology, 2011-10, Vol.9 (1), p.71-71, Article 71

2011

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Identification of high-affinity inhibitors of SARS-CoV-2 main protease: Towards the development of effective COVID-19 therapy

Virus research, 2020-10, Vol.288, p.198102-198102, Article 198102

2020

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Motional timescale predictions by molecular dynamics simulations: Case study using proline and hydroxyproline sidechain dynamics

Proteins, structure, function, and bioinformatics, 2014-02, Vol.82 (2), p.195-215

2014

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Studies on conformational changes induced by binding of pendimethalin with human serum albumin

Chemosphere (Oxford), 2020-03, Vol.243, p.125270, Article 125270

2020

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Exploring the interaction of a potent anti‐cancer drug Selumetinib with bovine serum albumin: Spectral and computational attributes

Journal of molecular recognition, 2024-07, Vol.37 (4), p.e3084-n/a

2024

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A comprehensive insight into the effects of caffeic acid (CA) on pepsin: Multi-spectroscopy and MD simulations methods

Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy, 2023-03, Vol.289, p.122240, Article 122240

2023

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Molecular dynamic simulation of wild type and mutants of the polymorphic amyloid NNQNTF segments of elk prion: Structural stability and thermodynamic of association

Biopolymers, 2011-09, Vol.95 (9), p.573-590

2011

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Investigation of molecular mechanisms of interaction between myofibrillar proteins and 1-heptanol by multiple spectroscopy and molecular docking methods

International journal of biological macromolecules, 2021-12, Vol.193 (Pt A), p.672-680

2021

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Identification of molecular descriptors for design of novel Isoalloxazine derivatives as potential Acetylcholinesterase inhibitors against Alzheimer's disease

Journal of biomolecular structure & dynamics, 2017-06, Vol.35 (8), p.1729-1742

2017

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In silico design and molecular basis for the selectivity of Olinone toward the first over the second bromodomain of BRD4

Proteins, structure, function, and bioinformatics, 2020-03, Vol.88 (3), p.414-430

2020

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Conformational landscapes of membrane proteins delineated by enhanced sampling molecular dynamics simulations

Biochimica et biophysica acta. Biomembranes, 2018-04, Vol.1860 (4), p.909-926

2018

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Binding Mechanism of Inhibitors to BRD4 and BRD9 Decoded by Multiple Independent Molecular Dynamics Simulations and Deep Learning

Molecules (Basel, Switzerland), 2024-04, Vol.29 (8), p.1857

2024

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Noncovalent interactions of bovine trypsin with curcumin and effect on stability, structure, and function

Colloids and surfaces, B, Biointerfaces, 2019-11, Vol.183, p.110287-110287, Article 110287

2019

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Long-timescale atomistic simulations uncover loss-of-function mechanisms of uncharacterized Angiogenin mutants associated with ALS

Archives of biochemistry and biophysics, 2024-06, Vol.756, p.110000, Article 110000

2024

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Structure-Based Virtual Screening Identifies Multiple Stable Binding Sites at the RecA Domains of SARS-CoV-2 Helicase Enzyme

Molecules (Basel, Switzerland), 2021-03, Vol.26 (5), p.1446

2021

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Disordered linkers in multidomain allosteric proteins: Entropic effect to favor the open state or enhanced local concentration to favor the closed state?

MD simulations reveal alternate conformations of the oxyanion hole in the Zika virus NS2B/NS3 protease

Identification of a conserved 8 aa insert in the PIP5K protein in the Saccharomycetaceae family of fungi and the molecular dynamics simulations and structural analysis to investigate its potential functional role

Atomic-level characterization of protein–protein association

Structural and Evolutionary Analysis Indicate That the SARS-CoV-2 Mpro Is a Challenging Target for Small-Molecule Inhibitor Design

Deciphering the crucial molecular properties of a series of Benzothiazole Hydrazone inhibitors that targets anti-apoptotic Bcl-xL protein

Interaction of novel Aurora kinase inhibitor MK-0457 with human serum albumin: Insights into the dynamic behavior, binding mechanism, conformation and esterase activity of human serum albumin

Aβ Monomers Transiently Sample Oligomer and Fibril-Like Configurations: Ensemble Characterization Using a Combined MD/NMR Approach

The interaction of Naphthol Yellow S (NYS) with pepsin: Insights from spectroscopic to molecular dynamics studies

Advances in computational methods for ligand binding kinetics

Molecular dynamics simulations and drug discovery

Identification of high-affinity inhibitors of SARS-CoV-2 main protease: Towards the development of effective COVID-19 therapy

Motional timescale predictions by molecular dynamics simulations: Case study using proline and hydroxyproline sidechain dynamics

Studies on conformational changes induced by binding of pendimethalin with human serum albumin

Exploring the interaction of a potent anti‐cancer drug Selumetinib with bovine serum albumin: Spectral and computational attributes

A comprehensive insight into the effects of caffeic acid (CA) on pepsin: Multi-spectroscopy and MD simulations methods

Molecular dynamic simulation of wild type and mutants of the polymorphic amyloid NNQNTF segments of elk prion: Structural stability and thermodynamic of association

Investigation of molecular mechanisms of interaction between myofibrillar proteins and 1-heptanol by multiple spectroscopy and molecular docking methods

Identification of molecular descriptors for design of novel Isoalloxazine derivatives as potential Acetylcholinesterase inhibitors against Alzheimer's disease

In silico design and molecular basis for the selectivity of Olinone toward the first over the second bromodomain of BRD4

Conformational landscapes of membrane proteins delineated by enhanced sampling molecular dynamics simulations

Binding Mechanism of Inhibitors to BRD4 and BRD9 Decoded by Multiple Independent Molecular Dynamics Simulations and Deep Learning

Noncovalent interactions of bovine trypsin with curcumin and effect on stability, structure, and function

Long-timescale atomistic simulations uncover loss-of-function mechanisms of uncharacterized Angiogenin mutants associated with ALS

Structure-Based Virtual Screening Identifies Multiple Stable Binding Sites at the RecA Domains of SARS-CoV-2 Helicase Enzyme

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