Somayah Albaradei^1,2,*

CMES-Computer Modeling in Engineering & Sciences, Vol.145, No.3, pp. 2937-2970, 2025, DOI:10.32604/cmes.2025.072584 - 23 December 2025

Abstract Cancer deaths and new cases worldwide are projected to rise by 47% by 2040, with transitioning countries experiencing an even higher increase of up to 95%. Tumor severity is profoundly influenced by the timing, accuracy, and stage of diagnosis, which directly impacts clinical decision-making. Various biological entities, including genes, proteins, mRNAs, miRNAs, and metabolites, contribute to cancer development. The emergence of multi-omics technologies has transformed cancer research by revealing molecular alterations across multiple biological layers. This integrative approach supports the notion that cancer is fundamentally driven by such alterations, enabling the discovery of molecular signatures… More > Graphic Abstract

XIANG LI^1,#, WENKE JIN^2,#, LIFENG WU², HUAN WANG¹, XIN XIE¹, WEI HUANG^1,*, BO LIU^2,*

Oncology Research, Vol.33, No.1, pp. 67-81, 2025, DOI:10.32604/or.2024.055921 - 20 December 2024

Abstract Background: Triple-negative breast cancer (TNBC), characterized by its lack of traditional hormone receptors and HER2, presents a significant challenge in oncology due to its poor response to conventional therapies. Autophagy is an important process for maintaining cellular homeostasis, and there are currently autophagy biomarkers that play an effective role in the clinical treatment of tumors. In contrast to targeting protein activity, intervention with protein-protein interaction (PPI) can avoid unrelated crosstalk and regulate the autophagy process with minimal interference pathways. Methods: Here, we employed Naive Bayes, Decision Tree, and k-Nearest Neighbors to elucidate the complex PPI… More >

MOHD ATHAR^1,*, ANU MANHAS², NISARG RANA², AHMAD IRFAN³

BIOCELL, Vol.48, No.6, pp. 935-944, 2024, DOI:10.32604/biocell.2024.049891 - 10 June 2024

Abstract Computational methods have significantly transformed biomedical research, offering a comprehensive exploration of disease mechanisms and molecular protein functions. This article reviews a spectrum of computational tools and network analysis databases that play a crucial role in identifying potential interactions and signaling networks contributing to the onset of disease states. The utilization of protein/gene interaction and genetic variation databases, coupled with pathway analysis can facilitate the identification of potential drug targets. By bridging the gap between molecular-level information and disease understanding, this review contributes insights into the impactful utilization of computational methods, paving the way for More >

Yao SUN, Yao LI, Xin SUN, Qiong WU, Lei WANG^*

BIOCELL, Vol.44, No.1, pp. 117-126, 2020, DOI:10.32604/biocell.2020.08242 - 01 March 2020

Abstract Phosphorylation is a common type of post-translational modification (PTM). It plays a vital role in many cellular processes. The reversible phosphorylation and dephosphorylation affect protein structures and proteinprotein interactions. Previously, we obtained five proteins that interact with ethylene-responsive factor (ERF) from the cDNA library of Populus simonii x Populus nigra. To further investigate the effect of dephosphorylation of PsnERF on its protein binding ability, we generated different phosphorylation states of PsnERF and demonstrated their protein binding capacity by the yeast two-hybrid assay (Y2H). The secondary structures and 3D structures of PsnERF, ERFm, TrunERF, and psnerf^197/198/202a were predicted More >

Chenyi An¹, Wei Chen^2,*

Molecular & Cellular Biomechanics, Vol.16, Suppl.2, pp. 109-110, 2019, DOI:10.32604/mcb.2019.07634

Abstract Biomembrane force probe (BFP) is a single-molecule biomechanical technique that has been widely used to characterize protein dynamics (e.g., protein-protein interactions and protein conformational changes), especially suitable for measuring force-regulated receptor-ligand binding kinetics in situ[1-4]. Integrated with various force spectroscopies, such as lifetime assay, it has become a powerful platform to systematically characterize many force-regulated receptor-ligand dissociation of great biological significance, which cannot be done with traditional solution based assays (e.g., surface plasma resonance) [5].
Even though the BFP has been quite successful in characterizing binding kinetics of weak and transient molecular interactions, it is… More >