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Molecular Modeling Connect

ISSN: 3006-9084
Volumes

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Articles

 
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
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

Limited information is currently available regarding the contraction mechanism of the Hcp-1 hemolysin-coregulated protein within the type VI secretion system (T6SS) of Acinetobacter baumannii, particularly about the secretion of toxic effectors. This research aimed to evaluate the mechanism underlying the contraction of the Hcp1 nanotube in response to the putative toxic effector TagX protein by employing bioinformatics tools and the artificial intelligence (AI) DeepMind system. To achieve this goal, the..

Journal: Molecular Modeling Connect
Editorial

Published: 07 Jul 2025

The Predictive Revolution: Rethinking Science Through Molecular Modeling

Volume 2

Journal: Molecular Modeling Connect
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
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 1

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
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
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
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
Research Article

Published: 26 Dec 2024

Study of the 3-(3,3-Dimethylbutanoyl)-4-hydroxy-6-neopentyl-2H-pyran-2-one by IR, Raman spectroscopy, and DFT

Volume 1

The heterocyclic structure of pyrones has a variety of biological activities and plays an important role in the creation of new drugs. Therefore, the study of the structure and spectra of pyrones is of considerable interest. In this work, the IR and Raman spectra of 3-(3,3-Dimethylbutanoyl)-4-hydroxy-6-neopentyl-2H-pyran-2-one (1) in its crystalline state was studied. The tautomerization of 1 was followed by a quantum-chemical method at the DFT/B3LYP/6-311G** level. The calculation for..

Journal: Molecular Modeling Connect
Research Article

Published: 17 Oct 2024

In Silico Investigation of the Constituents of Aroeira Honey (Astronium urundeuva) and the Binding Affinity with Important Proteins of M. leprae and M. tuberculosis

Volume 1

Journal: Molecular Modeling Connect
Editorial

Published: 11 Jul 2025

Preface

Volume 1

Welcome to the inaugural volume of MolMod Connect—a dynamic, peer-reviewed, open-access journal dedicated to advancing the frontiers of molecular modeling and simulation. Published biannually in print and online, MolMod Connect offers an inclusive and thoughtfully curated platform for high-quality research that pushes the boundaries of knowledge and innovation in this rapidly evolving field. Molecular modeling has sparked what can be described as a predictive revolution in science, enabling researchers worldwide..

Journal: Molecular Modeling Connect
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