AIMC Topic: Molecular Dynamics Simulation

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Insights into the Interaction Mechanisms of Peptide and Non-Peptide Inhibitors with MDM2 Using Gaussian-Accelerated Molecular Dynamics Simulations and Deep Learning.

Molecules (Basel, Switzerland)
Inhibiting MDM2-p53 interaction is considered an efficient mode of cancer treatment. In our current study, Gaussian-accelerated molecular dynamics (GaMD), deep learning (DL), and binding free energy calculations were combined together to probe the bi...

In Silico drug repurposing pipeline using deep learning and structure based approaches in epilepsy.

Scientific reports
Due to considerable global prevalence and high recurrence rate, the pursuit of effective new medication for epilepsy treatment remains an urgent and significant challenge. Drug repurposing emerges as a cost-effective and efficient strategy to combat ...

MDFit: automated molecular simulations workflow enables high throughput assessment of ligands-protein dynamics.

Journal of computer-aided molecular design
Molecular dynamics (MD) simulation is a powerful tool for characterizing ligand-protein conformational dynamics and offers significant advantages over docking and other rigid structure-based computational methods. However, setting up, running, and an...

Computational approaches for lead compound discovery in dipeptidyl peptidase-4 inhibition using machine learning and molecular dynamics techniques.

Computational biology and chemistry
The prediction of possible lead compounds from already-known drugs that may present DPP-4 inhibition activity imply a advantage in the drug development in terms of time and cost to find alternative medicines for the treatment of Type 2 Diabetes Melli...

Molecular docking aided machine learning for the identification of potential VEGFR inhibitors against renal cell carcinoma.

Medical oncology (Northwood, London, England)
Renal cell carcinoma is a highly vascular tumor associated with vascular endothelial growth factor (VEGF) expression. The Vascular Endothelial Growth Factor -2 (VEGF-2) and its receptor was identified as a potential anti-cancer target, and it plays a...

Machine Learning Prediction of Small Molecule Accumulation in Enhanced with Descriptor Statistics.

Journal of chemical theory and computation
Antibiotic resistance, particularly among Gram-negative bacteria, poses a significant healthcare challenge due to their ability to evade antibiotic action through various mechanisms. In this study, we explore the prediction of small molecule accumula...

RevGraphVAMP: A protein molecular simulation analysis model combining graph convolutional neural networks and physical constraints.

Methods (San Diego, Calif.)
Molecular dynamics simulation is a crucial research domain within the life sciences, focusing on comprehending the mechanisms of biomolecular interactions at atomic scales. Protein simulation, as a critical subfield, often utilizes MD for implementat...

Synthesis, Docking, and Machine Learning Studies of Some Novel Quinolinesulfonamides-Triazole Hybrids with Anticancer Activity.

Molecules (Basel, Switzerland)
In the presented work, a series of 22 hybrids of 8-quinolinesulfonamide and 1,4-disubstituted triazole with antiproliferative activity were designed and synthesised. The title compounds were designed using molecular modelling techniques. For this pur...

Accurate Prediction of Protein Structural Flexibility by Deep Learning Integrating Intricate Atomic Structures and Cryo-EM Density Information.

Nature communications
The dynamics of proteins are crucial for understanding their mechanisms. However, computationally predicting protein dynamic information has proven challenging. Here, we propose a neural network model, RMSF-net, which outperforms previous methods and...