“…We apply OPUS-Rota4 on 15 FM predictions submitted by AlphaFold2 on CASP14, the results show that the side chains modeled by OPUS-Rota4 are closer to their native counterparts than those predicted by AlphaFold2 (e.g. the residue-wise RMSD for all residues and core residues are 0.588 and 0.472 for AlphaFold2, and 0.535 and 0.407 for OPUS-Rota4).…”
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“…This methodology contributed to the best model for one of the CASP14 oligomeric targets, H1065. AVAILABILITY AND IMPLEMENTATION: All scripts for predictions and analysis are available from https://github.com/ElofssonLab/bioinfo-toolbox/ and https://gitlab.com/ElofssonLab/benchmark5/. …”
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“…Quercetin, kaempferol, and isorhamnetin were identified as the key ingredients by constructing ingredient-target network, and TP53, AKT1, VEGFA, IL6, TNF, CASP3, and EGFR were selected as the key targets by constructing PPI network. …”
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“…The main molecular targets of S. barbata on NPC were EGFR, MYC, CASP3, CCND1, and ESR1. The main biological processes involved the binding of DNA-binding transcription factors, RNA polymerase II-specific DNA-binding transcription factors, ubiquitin-like protein ligases, and ubiquitin-protein ligases. …”
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“…In a qPCR gene expression analysis of our own samples, we found Fgf21, Pparg, Ppard, and Casp6 to be dysregulated by maternal obesity. Maternal obesity represents a looming threat to the liver health of future generations. …”
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“…The quality of each study included in this review was independently assessed using criteria developed by CASP to assess all study types. Sixty-two articles were deemed eligible for analysis. …”
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“…We distinguished the hub molecular targets within pathways such as TNF, GAPDH, MAPK3, MAPK1, EGFR, CASP3, MAPK8, mTOR, IL-2, and MAPK14. Five of the more highly active compounds (acacetin, kaempferol, luteolin, naringenin, and quercetin) have anti-inflammatory and antioxidative properties. …”
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“…The final experiment detected ten genes (EGF, AKT1, JUN, MAPK8, MAPK1, CASP3, FOS, VEGFA, EGFR, and MYC) and three compounds (quercetin, kaempferol, and beta- carotene) in the MAPK pathway. …”
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“…Topological analysis yielded 45 key targets of SGD in the treatment of AA, including IL-6, PTGS2, TNF, VEGFA, CCL2, IL-1B, CXCL8, CASP3, MPO, and IL-10. There were 324 GO entries obtained through GO biological process enrichment analysis, and 20 pathways were obtained through KEGG pathway enrichment analysis, involving the PI3K-Akt signaling pathway, osteoclast differentiation, and Jak-STAT signaling pathway. …”
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“…For other study types, appropriate tools such as CASP/QUIPS/Cochrane non-randomised studies tool will be used. …”
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“…The ten key genes are AKT1, TNF, IL6, TP53, IL1B, JUN, CASP3, STAT3, MMP9, and MAPK3. Meanwhile, quercetin (Mol000098), luteolin (Mol000006), and kaempferol (Mol000422) are the most important core active ingredients. …”
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“…The authors appraised each of the six articles using the Critical Appraisal Skills Programme Checklist (CASP) Tool. This tool allowed the authors to synthesize information based on the outcomes and determine the level of the evidence of each article in order to make evidence-based practice recommendations on implementing alarm management programs. …”
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“…Interaction network analysis among proteins revealed that IL1B, P2RX7, IFNB1, IFNB1, TNF, and CASP1 enhanced the network connectivity between the combined gene set of COVID-19 and MS associated with NOD-like receptor (NLR) signaling. …”
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“…In addition, CD38 deficiency not only activated the transcription of Sirtuin-1 (SIRT1), but also inhibited ROS level and the transcription of NLR Family Pyrin Domain Containing 3 (NLRP3). (4) Conclusion: (i) CD38 may participate in the TLR9/IFN-α/Mx1 pathway by activating the expression of TLR9 after PPV infected PK-15 cells; (ii) CD38 may activate the NLRP3/CASP1 pathway by increasing ROS level; (iii) CD38 deficiency activates the expression of SIRT1 and can prevent the normal proliferation of PPV.…”
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“…Similar conclusions were reached in comparing AlphaFold2 predictions and NMR structures for three targets from the Critical Assessment of Protein Structure Prediction (CASP). These results contradict the widely held misperception that AlphaFold cannot accurately model solution NMR structures. …”
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“…The identified potential therapeutic targets of HNK (PTTH) included CCND1, SIRT2, AURKB, VEGFA, HDAC1, CASP9, HSP90AA1, and HSP90AB1, which can potentially inhibit the cell cycle of mBCSCs. …”
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“…Moreover, the in vitro experiments had shown that Fusobacterium nucleatum (F.n) could affect the CASP6 expression, which was associated with the chemoresistance to 5-fluorouracil (5-Fu) in CRC. …”
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“…The top eight anti-HCC core targets were identified: SRC, EGFR, CASP3, MMP9, mTOR, HIF1A, ERBB2, and PPARG. GO enrichment analysis showed that nitazoxanide might have anti-HCC effects by affecting gene targets involved in multiple biological processes (BP) (protein phosphorylation, transmembrane receptor protein tyrosine kinase (RTKs) signaling pathway, positive regulation of MAP kinase activity, etc.). …”
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“…In addition, it showed a significant apoptotic activity against MCF-7 cells by upregulating the expression of p53, bax and casp3 and downregulating bcl2. Furthermore, NF-κB activity was abolished while the expression of TNfα was increased confirming the significant apoptotic effect of EGA-EML-APA. …”
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