AIMC Topic: Molecular Docking Simulation

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CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13.

Journal of chemical information and modeling
A critical assessment of computational hit-finding experiments (CACHE) challenge was conducted to predict ligands for the SARS-CoV-2 Nsp13 helicase RNA binding site, a highly conserved COVID-19 target. Twenty-three participating teams comprised of co...

PrankWeb 4: a modular web server for protein-ligand binding site prediction and downstream analysis.

Nucleic acids research
Knowledge of protein-ligand binding sites (LBSs) is crucial for advancing our understanding of biology and developing practical applications in fields such as medicine or biotechnology. PrankWeb is a web server that allows users to predict LBSs from ...

HawkDock version 2: an updated web server to predict and analyze the structures of protein-protein complexes.

Nucleic acids research
Protein-protein interactions (PPIs) are fundamental to cellular functions, yet predicting and analyzing their 3D structures remains a critical and computationally demanding challenge. To address this, the HawkDock web server was developed as an integ...

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 ...

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...

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...

Hugan Tiaoshen Formula Improves the Comorbid Mechanism of Schizophrenia and Sleep Disorder via Multitarget Interaction Network.

FASEB journal : official publication of the Federation of American Societies for Experimental Biology
This study aims to integrate cross-disease omics data and perform multidimensional analysis to uncover the molecular basis of schizophrenia (SCZ) and sleep disorder (SD) comorbidity and to systematically analyze the potential mechanism of the Hugan T...

ABP-Xplorer: A Machine Learning Approach for Prediction of Antibacterial Peptides Targeting -tRNA-Methyltransferase (TrmD).

Journal of chemical information and modeling
(MAB) infections pose a significant treatment challenge due to their intrinsic resistance to antibiotics, requiring prolonged multidrug regimens with limited success and frequent relapses. tRNA (m1G37) methyltransferase (TrmD), an enzyme essential f...