AIMC Topic: Molecular Dynamics Simulation
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In silico design strategies for tubulin inhibitors for the development of anticancer therapies.
Expert opinion on drug discovery
Aug 1, 2025
INTRODUCTION: Microtubules, composing of α, β-tubulin dimers, are important for cellular processes like proliferation and transport, thereby they become suitable targets for research in cancer. Existing candidates often exhibit off-target effects, ne...
In silico discovery of novel compounds for FAK activation using virtual screening, AI-based prediction, and molecular dynamics.
Computational biology and chemistry
Aug 1, 2025
Focal Adhesion Kinase (FAK) is a non-receptor tyrosine kinase that plays a crucial role in cell proliferation, migration, and signal transduction. FAK is overexpressed in metastatic and advanced-stage cancers, where it is considered a key kinase in c...
Machine Learning-Augmented Molecular Dynamics Simulations (MD) Reveal Insights Into the Disconnect Between Affinity and Activation of ZTP Riboswitch Ligands.
Angewandte Chemie (International ed. in English)
Jul 28, 2025
The challenge of targeting RNA with small molecules necessitates a better understanding of RNA-ligand interaction mechanisms. However, the dynamic nature of nucleic acids, their ligand-induced stabilization, and how conformational changes influence g...
Characterizing DNA Origami Nanostructures in TEM Images Using Convolutional Neural Networks.
Journal of chemical information and modeling
Jul 14, 2025
Artificial intelligence (AI) models remain an emerging strategy to accelerate materials design and development. We demonstrate that CNN models can characterize DNA origami nanostructures employed in programmable self-assembly, which is important in m...
Predicting rare DNA conformations via dynamical graphical models: a case study of the B→A transition.
Nucleic acids research
Jul 8, 2025
DNA exhibits local conformational preferences that affect its ability to adopt biologically relevant conformations, such as those required for binding proteins. Traditional methods, like Markov state models and molecular dynamics (MD) simulations, ha...
CGeNArateWeb: a web server for the atomistic study of the structure and dynamics of chromatin fibers.
Nucleic acids research
Jul 7, 2025
We present CGeNArateWeb, a new web tool for the three-dimensional simulation of naked DNA and protein-bound chromatin fibers. The server allows the user to obtain a dynamic representation of long segments of linear, circular, or protein-DNA segments ...
Computer-aided unveiling molecular mechanisms of Xylocarpus granatum against colorectal cancer: therapeutic intervention targeting P13K-AKT signaling pathway.
Computers in biology and medicine
Jul 1, 2025
Colorectal cancer (CRC) is a leading cause of cancer-related morbidity and mortality globally, with increasing incidence rates, particularly in early-onset cases. Despite advances in treatment, many developing countries face affordability and safety ...
Computational modelling of olfactory receptors.
Biochimica et biophysica acta. General subjects
Jul 1, 2025
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
Jul 1, 2025
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
Jul 1, 2025
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...
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