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Molecular Modeling Connect

ISSN: 3105-3734
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Volume 2

Articles

All Articles
open-access Editorial

Published: 29 Dec 2025

Preface

Volume 2

With the completion of Volume 2, Molecular Modeling Connect proudly marks its second year of contributions to the scientific community, representing another significant step forward in its mission to serve as a dynamic forum for the global molecular modeling community. This volume stands as a testament to the growing relevance of computational and theoretical approaches in shaping modern molecular science and to the enthusiasm of researchers who are advancing this..

Journal: Molecular Modeling Connect
open-access Research Article

Published: 30 Oct 2025

Unraveling Conformational Thermodynamics of Ligand Binding to Fluoride Riboswitch Aptamer: Implications for Therapeutic Design

Volume 2

Journal: Molecular Modeling Connect
open-access Research Article

Published: 25 Jul 2025

Structural and Molecular Changes of Isonicotinylhydrazine Anti-Tubercular Drug in Alcohol Environment: An Intuition from Theory

Volume 2

Journal: Molecular Modeling Connect
open-access Editorial

Published: 07 Jul 2025

The Predictive Revolution: Rethinking Science Through Molecular Modeling

Volume 2

Journal: Molecular Modeling Connect
open-access Research Article

Published: 30 Jun 2025

Effect of Acyl Chain Variation and Cholesterol on Structural and Dynamic Properties of Lipid Bilayer Probed by Simulation

Volume 2

Lipid ordering plays a crucial role in maintaining the mechanical strength of the lipid bilayer, which is influential in controlling biological functions. This is associated with the well-known phenomena of “phase state behavior” of the bilayer. The significant factors that influence phase state behavior are stimuli such as cholesterol, physiological conditions like temperature and pH, and the structure of the lipid molecule itself, which can differ either in the head..

Journal: Molecular Modeling Connect
open-access Research Article

Published: 27 Jun 2025

The Impact of Toxic Effector Molecule TagX on the Amino Acid Conformation of the Hcp1 Monohexameric Ring in Acinetobacter baumannii Type VI Secretion System Utilizing Bioinformatics Tools and an AI System

Volume 2

Journal: Molecular Modeling Connect
open-access Research Article

Published: 07 May 2025

Exploring Artesunate and Dihydroartemisinin for Mechanism on MMP-3 and MMP-13 via Molecular Docking and Molecular Dynamics

Volume 2

The application of natural products has drawn increasing attention in recent times. Artesunate (ART) and Dihydroartemisinin (DHA), being natural products with anti-inflammatory and cartilage protective capabilities, have shown potential in osteoarthritis (OA) treatment. OA is a highly prevalent degenerative joint disease globally, leading to a diminished quality of life and is a major cause of disability. Matrix metalloproteinase 3 (MMP-3) and MMP-13 play crucial roles in OA progression. Although ART..

Journal: Molecular Modeling Connect
open-access Research Article

Published: 04 Apr 2025

Smart Gas Sensing by (Al/C/Si)-Doped Boron Nitride Nanomaterial Towards Grabbing Nitric Oxide: A Novel Applied Technique for Air Pollution Reduction by DFT Analysis

Volume 2

The electronic, magnetic, and thermodynamic properties of adsorption of toxic gases, including Nitric oxide (NO) by using Y (Y = Al, C, Si)-doped boron nitride nanocage (BN) have been investigated using density functional theory (DFT). The results denote that NO→Y–BN are stable compounds, with the most stable adsorption site being the center of the cage ring. Furthermore, the reported results of nuclear magnetic resonance (NMR) spectroscopy have exhibited the strength..

Journal: Molecular Modeling Connect
open-access Research Article

Published: 20 Mar 2025

Food and Medicine Homology Substance in Cancer Treatment: Mechanism of Astragalus against Pancreatic Cancer

Volume 2

Journal: Molecular Modeling Connect
open-access Research Article

Published: 20 Mar 2025

Unusual Arrangement of Catalytic Loops of the Alcohol Dehydrogenase Enzyme During the Adsorption Process on a Graphitic Carbon Surface

Volume 2

Molecular dynamics simulations (MDs) were conducted to investigate the alcohol dehydrogenase (ADH) enzyme and its cofactor, nicotinamide adenine dinucleotide (NAD), solvated in an aqueous system on a graphite-carbon surface. The study focuses on key structural aspects of ADH, particularly its conformational changes, including the rotation of the catalytic domain, the coenzyme binding domain, and the rearrangement of the active center required for catalytic activation. MDs were performed for 100 ns..

Journal: Molecular Modeling Connect
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