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Ab Initio Molecular Dynamics: Basic Theory and Advanced Methods

1, 2009

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Integration of Molecular Docking Analysis and Molecular Dynamics Simulations for Studying Food Proteins and Bioactive Peptides

Journal of agricultural and food chemistry, 2022-02, Vol.70 (4), p.934-943

2022

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Molecular docking, validation, dynamics simulations, and pharmacokinetic prediction of natural compounds against the SARS-CoV-2 main-protease

Journal of biomolecular structure & dynamics, 2022-02, Vol.40 (2), p.585-611

2022

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Molecular Binding Mechanism and Pharmacology Comparative Analysis of Noscapine for Repurposing against SARS-CoV‑2 Protease

Journal of proteome research, 2020-11, Vol.19 (11), p.4678-4689

2020

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Computational Chemistry: Introduction to the Theory and Applications of Molecular and Quantum Mechanics

Lewars, Errol G

Third edition., 2016

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Molecular docking and molecular dynamics simulation approach to screen natural compounds for inhibition of Xanthomonas oryzae pv. Oryzae by targeting peptide deformylase

Journal of biomolecular structure & dynamics, 2021-02, Vol.39 (3), p.823-840

2021

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Molecular docking, molecular dynamics simulations and reactivity, studies on approved drugs library targeting ACE2 and SARS-CoV-2 binding with ACE2

Journal of biomolecular structure & dynamics, 2021-12, Vol.39 (18), p.7246-7262

2021

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More simple, efficient and accurate food research promoted by intermolecular interaction approaches: A review

Food chemistry, 2023-08, Vol.416, p.135726-135726, Article 135726

2023

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Probing intermolecular interactions and binding stability of kaempferol, quercetin and resveratrol derivatives with PPAR-γ: docking, molecular dynamics and MM/GBSA approach to reveal potent PPAR- γ agonist against cancer

Journal of biomolecular structure & dynamics, 2022-02, Vol.40 (3), p.971-981

2022

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High throughput virtual screening and molecular dynamics simulation analysis of phytomolecules against BfmR of Acinetobacter baumannii: anti-virulent drug development campaign

Journal of biomolecular structure & dynamics, 2023-05, Vol.41 (7), p.2698-2712

2023

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YASARA: A Tool to Obtain Structural Guidance in Biocatalytic Investigations

Methods in molecular biology (Clifton, N.J.), 2018, Vol.1685, p.43

2018

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De novo design of novel protease inhibitor candidates in the treatment of SARS-CoV-2 using deep learning, docking, and molecular dynamic simulations

Computers in biology and medicine, 2021-12, Vol.139, p.104967-104967, Article 104967

2021

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Screening of plant-based natural compounds as a potential COVID-19 main protease inhibitor: an in silico docking and molecular dynamics simulation approach

Journal of biomolecular structure & dynamics, 2022-02, Vol.40 (2), p.696-711

2022

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Potential inhibitors of SARS-cov-2 RNA dependent RNA polymerase protein: molecular docking, molecular dynamics simulations and MM-PBSA analyses

Journal of biomolecular structure & dynamics, 2022-01, Vol.40 (1), p.361-374

2022

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Insights into in-vitro studies and molecular modelling of the antimicrobial efficiency of 4-chlorobenzaldehyde and 4-methoxybenzaldehyde derivatives

Journal of biomolecular structure & dynamics, 2024-08, Vol.42 (12), p.6042-6064

2024

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Design, computational studies, synthesis and biological evaluation of thiazole-based molecules as anticancer agents

European journal of pharmaceutical sciences, 2019-06, Vol.134, p.20-30

2019

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Molecular modeling, docking and simulation dynamics of β-glucosidase reveals high-efficiency, thermo-stable, glucose tolerant enzyme in Paenibacillus lautus BHU3 strain

International journal of biological macromolecules, 2021-01, Vol.168, p.371-382

2021

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Mining of a novel esterase (est3S) gene from a cow rumen metagenomic library with organosphosphorus insecticides degrading capability: Catalytic insights by site directed mutations, docking, and molecular dynamic simulations

International journal of biological macromolecules, 2021-11, Vol.190, p.441-455

2021

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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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Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

Journal of computer-aided molecular design, 2017-01, Vol.31 (1), p.147-161

2017

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Discovery of new nicotinamides as apoptotic VEGFR-2 inhibitors: virtual screening, synthesis, anti-proliferative, immunomodulatory, ADMET, toxicity, and molecular dynamic simulation studies

Journal of enzyme inhibition and medicinal chemistry, 2022-12, Vol.37 (1), p.1389-1403

2022

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Phytochemicals-based targeting RdRp and main protease of SARS-CoV-2 using docking and steered molecular dynamic simulation: A promising therapeutic approach for Tackling COVID-19

Computers in biology and medicine, 2022-06, Vol.145, p.105468-105468, Article 105468

2022

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Anisotropic Friction in a Ligand-Protein Complex

Nano letters, 2023-05, Vol.23 (10), p.4111-4119

2023

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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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In silico assessments of the small molecular boron agents to pave the way for artificial intelligence-based boron neutron capture therapy

European journal of medicinal chemistry, 2024-12, Vol.279, p.116841, Article 116841

2024

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Ab Initio Molecular Dynamics: Basic Theory and Advanced Methods

Integration of Molecular Docking Analysis and Molecular Dynamics Simulations for Studying Food Proteins and Bioactive Peptides

Molecular docking, validation, dynamics simulations, and pharmacokinetic prediction of natural compounds against the SARS-CoV-2 main-protease

Molecular Binding Mechanism and Pharmacology Comparative Analysis of Noscapine for Repurposing against SARS-CoV‑2 Protease

Computational Chemistry: Introduction to the Theory and Applications of Molecular and Quantum Mechanics

Molecular docking and molecular dynamics simulation approach to screen natural compounds for inhibition of Xanthomonas oryzae pv. Oryzae by targeting peptide deformylase

Molecular docking, molecular dynamics simulations and reactivity, studies on approved drugs library targeting ACE2 and SARS-CoV-2 binding with ACE2

More simple, efficient and accurate food research promoted by intermolecular interaction approaches: A review

Probing intermolecular interactions and binding stability of kaempferol, quercetin and resveratrol derivatives with PPAR-γ: docking, molecular dynamics and MM/GBSA approach to reveal potent PPAR- γ agonist against cancer

High throughput virtual screening and molecular dynamics simulation analysis of phytomolecules against BfmR of Acinetobacter baumannii: anti-virulent drug development campaign

YASARA: A Tool to Obtain Structural Guidance in Biocatalytic Investigations

De novo design of novel protease inhibitor candidates in the treatment of SARS-CoV-2 using deep learning, docking, and molecular dynamic simulations

Screening of plant-based natural compounds as a potential COVID-19 main protease inhibitor: an in silico docking and molecular dynamics simulation approach

Potential inhibitors of SARS-cov-2 RNA dependent RNA polymerase protein: molecular docking, molecular dynamics simulations and MM-PBSA analyses

Insights into in-vitro studies and molecular modelling of the antimicrobial efficiency of 4-chlorobenzaldehyde and 4-methoxybenzaldehyde derivatives

Design, computational studies, synthesis and biological evaluation of thiazole-based molecules as anticancer agents

Molecular modeling, docking and simulation dynamics of β-glucosidase reveals high-efficiency, thermo-stable, glucose tolerant enzyme in Paenibacillus lautus BHU3 strain

Mining of a novel esterase (est3S) gene from a cow rumen metagenomic library with organosphosphorus insecticides degrading capability: Catalytic insights by site directed mutations, docking, and molecular dynamic simulations

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

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

Discovery of new nicotinamides as apoptotic VEGFR-2 inhibitors: virtual screening, synthesis, anti-proliferative, immunomodulatory, ADMET, toxicity, and molecular dynamic simulation studies

Phytochemicals-based targeting RdRp and main protease of SARS-CoV-2 using docking and steered molecular dynamic simulation: A promising therapeutic approach for Tackling COVID-19

Anisotropic Friction in a Ligand-Protein Complex

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

In silico assessments of the small molecular boron agents to pave the way for artificial intelligence-based boron neutron capture therapy

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