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Unraveling the unbinding pathways of SARS-CoV-2 Papain-like proteinase known inhibitors by Supervised Molecular Dynamics simulation

PloS one, 2021-05, Vol.16 (5), p.e0251910-e0251910

2021

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Comparative analysis of the unbinding pathways of antiviral drug Indinavir from HIV and HTLV1 proteases by supervised molecular dynamics simulation

PloS one, 2021-09, Vol.16 (9), p.e0257916

2021

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A boosted unbiased molecular dynamics method for predicting ligands binding mechanisms: probing the binding pathway of dasatinib to Src-kinase

Bioinformatics, 2020-09, Vol.36 (18), p.4714-4720

2020

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pH-dependence of the Plasmodium falciparum chloroquine resistance transporter is linked to the transport cycle

Nature communications, 2023-07, Vol.14 (1), p.4234-4234, Article 4234

2023

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Rational drug repurposing for cancer by inclusion of the unbiased molecular dynamics simulation in the structure-based virtual screening approach: Challenges and breakthroughs

Seminars in cancer biology, 2021-01, Vol.68, p.249-257

2021

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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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Characterization of the Bottlenecks and Pathways for Inhibitor Dissociation from [NiFe] Hydrogenase

Journal of chemical information and modeling, 2024-05, Vol.64 (10), p.4193-4203

2024

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Application of Molecular Dynamics in Coating Ag-Conjugated Nanoparticles with Potential Therapeutic Applications

Nano biomedicine and engineering, 2020-03, Vol.12 (1), p.90-98

2020

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Reconstruction of the binding pathway of an anti-HIV drug, Indinavir, in complex with the HTLV-1 protease using unaggregated unbiased molecular dynamics simulation

Computational biology and chemistry, 2022-02, Vol.96, p.107616-107616, Article 107616

2022

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Repurposing existing drugs for new AMPK activators as a strategy to extend lifespan: a computer-aided drug discovery study

Biogerontology (Dordrecht), 2018-04, Vol.19 (2), p.133-143

2018

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Complete reconstruction of dasatinib unbinding pathway from c-Src kinase by supervised molecular dynamics simulation method; assessing efficiency and trustworthiness of the method

Journal of biomolecular structure & dynamics, 2022-01, Vol.40 (23), p.12535-12545

2022

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Prediction of new chromene-based inhibitors of tubulin using structure-based virtual screening and molecular dynamics simulation methods

Computational biology and chemistry, 2017-12, Vol.71, p.89-97

2017

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In silico prediction of new inhibitors for the nucleotide pool sanitizing enzyme, MTH1, using drug repurposing

Journal of biomolecular structure & dynamics, 2018-07, Vol.36 (10), p.2628-2636

2018

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In silico drug repurposing of FDA-approved drugs to predict new inhibitors for drug resistant T315I mutant and wild-type BCR-ABL1: A virtual screening and molecular dynamics study

Journal of molecular graphics & modelling, 2017-06, Vol.74, p.234-240

2017

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Unraveling the unbinding pathways of SARS-CoV-2 Papain-like proteinase known inhibitors by Supervised Molecular Dynamics simulation

Comparative analysis of the unbinding pathways of antiviral drug Indinavir from HIV and HTLV1 proteases by supervised molecular dynamics simulation

A boosted unbiased molecular dynamics method for predicting ligands binding mechanisms: probing the binding pathway of dasatinib to Src-kinase

pH-dependence of the Plasmodium falciparum chloroquine resistance transporter is linked to the transport cycle

Rational drug repurposing for cancer by inclusion of the unbiased molecular dynamics simulation in the structure-based virtual screening approach: Challenges and breakthroughs

Advances in computational methods for ligand binding kinetics

Characterization of the Bottlenecks and Pathways for Inhibitor Dissociation from [NiFe] Hydrogenase

Application of Molecular Dynamics in Coating Ag-Conjugated Nanoparticles with Potential Therapeutic Applications

Reconstruction of the binding pathway of an anti-HIV drug, Indinavir, in complex with the HTLV-1 protease using unaggregated unbiased molecular dynamics simulation

Repurposing existing drugs for new AMPK activators as a strategy to extend lifespan: a computer-aided drug discovery study

Complete reconstruction of dasatinib unbinding pathway from c-Src kinase by supervised molecular dynamics simulation method; assessing efficiency and trustworthiness of the method

Prediction of new chromene-based inhibitors of tubulin using structure-based virtual screening and molecular dynamics simulation methods

In silico prediction of new inhibitors for the nucleotide pool sanitizing enzyme, MTH1, using drug repurposing

In silico drug repurposing of FDA-approved drugs to predict new inhibitors for drug resistant T315I mutant and wild-type BCR-ABL1: A virtual screening and molecular dynamics study

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