AIMC Topic: Molecular Dynamics Simulation

Clear Filters Showing 621 to 630 of 710 articles

Computational modelling of olfactory receptors.

Biochimica et biophysica acta. General subjects
Olfactory receptors (ORs), the largest subfamily of G protein-coupled receptors, are essential for detecting and interpreting environmental odorants in animals. Understanding their function is crucial for deciphering olfactory perception and explorin...

On the application of artificial intelligence in virtual screening.

Expert opinion on drug discovery
INTRODUCTION: Artificial intelligence (AI) has emerged as a transformative tool in drug discovery, particularly in virtual screening (VS), a crucial initial step in identifying potential drug candidates. This article highlights the significance of AI...

Identification and designing an analgesic opioid cyclic peptide from Defensin 4 of Mesobuthus martensii Karsch scorpion venom with more effectiveness than morphine.

Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie
Considering the limitations of use and side effects of existing analgesics, the discovery of new analgesics is necessary. Venoms of organisms are an important source of analgesic peptides. In this study, using computational biology methods such as mo...

SympGNNs: Symplectic Graph Neural Networks for identifying high-dimensional Hamiltonian systems and node classification.

Neural networks : the official journal of the International Neural Network Society
Existing neural network models to learn Hamiltonian systems, such as SympNets, although accurate in low-dimensions, struggle to learn the correct dynamics for high-dimensional many-body systems. Herein, we introduce Symplectic Graph Neural Networks (...

When Simulations Meet Machine Learning: Redefining Molecular Docking for Protein-Glycosaminoglycan Systems.

Journal of computational chemistry
Glycosaminoglycans (GAGs) are linear, negatively charged carbohydrates that modulate enzymatic activity in the extracellular matrix. Their high flexibility and specificity in protein-GAG interactions pose challenges for both experimental and computat...

NepoIP/MM: Toward Accurate Biomolecular Simulation with a Machine Learning/Molecular Mechanics Model Incorporating Polarization Effects.

Journal of chemical theory and computation
Machine learning force fields offer the ability to simulate biomolecules with quantum mechanical accuracy while significantly reducing computational costs, attracting a growing amount of attention in biophysics. Meanwhile, by leveraging the efficienc...

Active Learning-Guided Hit Optimization for the Leucine-Rich Repeat Kinase 2 WDR Domain Based on In Silico Ligand-Binding Affinities.

Journal of chemical information and modeling
The leucine-rich repeat kinase 2 (LRRK2) is the most mutated gene in familial Parkinson's disease, and its mutations lead to pathogenic hallmarks of the disease. The LRRK2 WDR domain is an understudied drug target for Parkinson's disease, with no kno...

Investigating the Nature of PRM:SH3 Interactions Using Artificial Intelligence and Molecular Dynamics.

Journal of chemical information and modeling
Understanding the binding interactions within protein-peptide complexes is crucial for elucidating key physicochemical phenomena in biological systems. Among the outcomes of these interactions, biomolecular condensates have recently emerged as vital ...

Using Machine Learning to Analyze Molecular Dynamics Simulations of Biomolecules.

The journal of physical chemistry. B
Machine learning (ML) techniques have become powerful tools in both industrial and academic settings. Their ability to facilitate analysis of complex data and generation of predictive insights is transforming how scientific problems are approached ac...

Rational Design of an Epoxide Hydrolase From Spatholobus Suberectus: Enhancing Catalytic Activity and Thermostability for Efficient (R)-Styrene Oxide Production.

Biotechnology journal
(R)-Styrene oxide is a high-value chiral intermediate in pharmaceutical and chemical industries, yet its enantioselective synthesis remains challenging. Here, we engineered an epoxide hydrolase from Spatholobus suberectus (SsEH) to address its limita...