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Computational algorithms and tools have retrenched the drug discovery and development timeline. The applicability of computational approaches has gained immense relevance owing to the dramatic surge in the structural information of biomacromolecules and their heteromolecular complexes. Computational methods are now extensively used in identifying new protein targets, druggability assessment, pharmacophore mapping, molecular docking, the virtual screening of lead molecules, bioactivity prediction, molecular dynamics of protein-ligand complexes, affinity prediction, and for designing better ligands. Herein, we provide an overview of salient components of recently reported computational drug-discovery workflows that includes algorithms, tools, and databases for protein target identification and optimized ligand selection.
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http://dx.doi.org/10.1039/d4md00223g | DOI Listing |
J Environ Pathol Toxicol Oncol
January 2025
Department of Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing 210009, China.
Noncoding RNA regulatory networks play crucial roles in human breast cancer. The aim of this study was to establish a network containing multi-type RNAs and RBPs in triple-negative breast cancer (TNBC). Differential expression analyses of lncRNAs, miRNAs, and genes were performed using the GEO2R tool.
View Article and Find Full Text PDFChem Biodivers
September 2025
Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, Punjab, India.
Argemone mexicana is one of the known herbaceous plants hosting bioactive isoquinoline alkaloids. In the current study, an endophytic fungal isolate was studied for anti-inflammatory potential and the identification of its bioactive molecule. An endophytic fungus AMEF-14 was obtained from this plant and identified as Cladosporium ramotenellum based on microscopy and molecular tools.
View Article and Find Full Text PDFPostgrad Med J
September 2025
Department of Basic Medicine, Shantou University Medical College, 22 Xinling Road, Jinping District, Shantou, Guangdong, 515041, China.
Background: Coronary atherosclerosis is a leading cause of cardiovascular disease and death worldwide. Despite progress in understanding its pathogenesis, the roles of circulating inflammatory proteins and plasma metabolites are complex and not fully elucidated. Existing Mendelian randomization (MR) studies often target isolated biomarkers, lacking comprehensive and mechanistic insights.
View Article and Find Full Text PDFAm J Respir Cell Mol Biol
September 2025
Univ. of Pennsylvania, Medicine, Philadelphia, Pennsylvania, United States.
Lymphangioleiomyomatosis (LAM) is a rare lung disease caused by hyperactivation of the mechanistic/mammalian target of rapamycin 1 (mTORC1) growth pathway in a subset of mesenchymal lung cells. Histopathologically, LAM lesions have been described as immature smooth muscle-like cells positive for the immature melanocytic marker HMB45/PMEL/gp100 and phosphorylated ribosomal protein S6 (pS6). Advances in single cell sequencing (scRNA-seq) technology allowed us to group LAM cells according to their expression of cancer stem cell (CSC) genes and identify three clusters: a high CSC-like state (SLS), an intermediate state, and a low CSC-like inflammatory state (IS).
View Article and Find Full Text PDFProc Natl Acad Sci U S A
September 2025
Department of Ophthalmology, Tianjin Medical University General Hospital, International Joint Laboratory of Ocular Diseases (Ministry of Education), State Key Laboratory of Experimental Hematology, Tianjin Key Laboratory of Ocular Trauma, Laboratory of Molecular Ophthalmology, Tianjin Medical Univer
Ocular fibrosis, a severe consequence of excessive retinal wound healing, can lead to vision loss following retinal injury. Proliferative vitreoretinopathy (PVR), a common form of ocular fibrosis, is a major cause of blindness, characterized by the formation of extensive fibrous proliferative membranes. Understanding the cellular origins of PVR-associated fibroblasts (PAFs) is essential to decipher the mechanisms of ocular wound healing.
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