As protein-protein interactions are crucial in most biological processes, it is valuable to understand how and where protein pairs interact. We developed a web server HOMCOS (Homology Modeling of Complex Structure, http://biunit.naist.jp/homcos) to predict interacting protein pairs and interacting sites by homology modeling of complex structures. Our server is capable of three services. The first is modeling heterodimers from two query amino acid sequences posted by users. The server performs BLAST searches to identify homologous templates in the latest representative dataset of heterodimer structures generated from the PQS database. Structure validity is evaluated by the combination of sequence similarity and knowledge-based contact potential energy as previously described. The server generates a sequence-replaced model PDB file and a MODELLER script to build full atomic models of complex structures. The second service is modeling homodimers from one query sequence. The third service is identification of potentially interacting proteins for one query sequence. The server searches the dataset of heterodimer structures for a homologous template, outputs the candidate interacting sequences in the Uniprot database homologous for the interacting partner template proteins. These features are useful for wide range of researchers to predict putative interaction sites and interacting proteins.
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http://dx.doi.org/10.1093/nar/gkn218 | DOI Listing |
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April 2024
Institut für Parasitologie, Biomedizinisches Forschungszentrum Seltersberg (BFS), Justus Liebig Universitaet Giessen, Giessen, Germany.
Introduction: Schistosomiasis has for many years relied on a single drug, praziquantel (PZQ) for treatment of the disease. Immense efforts have been invested in the discovery of protein kinase (PK) inhibitors; however, given that the majority of PKs are still not targeted by an inhibitor with a useful level of selectivity, there is a compelling need to expand the chemical space available for synthesizing new, potent, and selective PK inhibitors. Small-molecule inhibitors targeting the ATP pocket of the catalytic domain of PKs have the potential to become drugs devoid of (major) side effects, particularly if they bind selectively.
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April 2024
Centre for Malaria Elimination, Institute of Tropical Medicine, Mount Kenya University, Thika, Kenya.
The Circumsporozoite Protein (PfCSP) has been used in developing the RTS,S, and R21 malaria vaccines. However, genetic polymorphisms within compromise the effectiveness of the vaccine. Thus, it is essential to continuously assess the genetic diversity of , especially when deploying it across different geographical regions.
View Article and Find Full Text PDFTransl Cancer Res
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Medical College of Qinghai University, Xining, China.
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View Article and Find Full Text PDFNarra J
December 2024
Doctoral Program of Medical Science, Faculty of Medicine, Universitas Sebelas Maret Surakarta, Indonesia.
Osteoporosis increases fracture risk and reduces quality of life in menopausal women. Although physical activity, such as walking and bone joint exercise, is known to help maintain bone health, its effectiveness needs further examination. The aim of this study was to analyze the effects of physical activity, in particular walking and bone joint exercise, on enhancing bone remodeling in menopausal women.
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