AIMC Topic: Molecular Dynamics Simulation

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PEGASUS: Prediction of MD-derived protein flexibility from sequence.

Protein science : a publication of the Protein Society
Protein flexibility is essential to its biological function. However, experimental methods for its assessment, such as X-ray crystallography and nuclear magnetic resonance spectroscopy, are often limited by experimental variability and high cost, lea...

Discovery of novel potential 11β-HSD1 inhibitors through combining deep learning, molecular modeling, and bio-evaluation.

Molecular diversity
11β-Hydroxysteroid dehydrogenase type 1 (11β-HSD1) has been shown to play an important role in the treatment of impaired glucose tolerance, insulin resistance, dyslipidemia, and obesity and is a promising drug target. In this study, we built a gated ...

First report on analysis of chemical space, scaffold diversity, critical structural features of HDAC11 inhibitors.

Molecular diversity
In the histone deacetylase (HDAC) family, HDAC11 is the smallest and a single member under the class IV subtype. It is important as a drug target mainly in cancer, inflammatory and autoimmune diseases. The design and development of selective HDAC11 i...

In silico design strategies for tubulin inhibitors for the development of anticancer therapies.

Expert opinion on drug discovery
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
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)
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
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
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
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
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 ...