If there was no protein with binding score less than 0, the motifs of the proteins whose scores ranked in the top 2000 were taken to form the motif database. After obtaining the motif databases, we applied the 2DPPI-Miner to calculate and score the possibilities of binding between the ...
The basic idea of the algorithm is to form a low-dimensional vector space by extracting features from a graph by both a breadth-first search and a depth-first search. Node2vec applies two parameters to implement the strategy of random walk. Return Parameter pp controls the probability of the...
Chitin, the main form of aminated polysaccharide in nature, is a biocompatible, polycationic, and antimicrobial biopolymer used extensively in industrial processes. Despite the abundance of chitin, applications thereof are hampered by difficulties in feedstock harvesting and limited structural versatility....
Ferroptosis is a newly identified iron-dependent form of death that is becoming increasingly recognized as a promising avenue for cancer therapy. N6-methyladenosine (m6A) is the most abundant reversible methylation modification in mRNA contributing to tumorigenesis. However, the crucial role of m6A modi...
Steroid-resistant asthma (SRA) is a form of asthma resistant to corticosteroid therapy, which is characterized by the presence of neutrophil-predominant inflammatory response and neutrophil extracellular traps (NETs) formation. Hyssopus cuspidatus Boriss., a traditional Uyghur medicine, is known for it...
This study utilizes nine types of atomic features and four types of bond features to characterize atoms and their local environments. The node features have a size of 44, while the edge features have a size of 14. Most of these features are encoded in one-hot form, while formal charge ...
Suanzaoren Decoction (SZRD), a well-known formula from traditional Chinese medicine, has been shown to have reasonable cognitive effects while relaxing and alleviating insomnia. Several studies have demonstrated significant therapeutic effects of SZRD on
Proper folding typically results in proteins existing in a soluble form within cells. If the folding rate is too slow or there are errors in the folding, it may cause the protein to exist in an insoluble form, leading to loss of protein function and even cause some diseases related to ...
C522 and the oxidized form CSD.522 (S-cysteinesulfinic acid) in resolved substructures, PDB data (Bioinformatics and for Structural. RCSB PDB - Protein Data Bank. 2025). In the genotypical lamin A Ig-fold (PDB: 1IFR (2002) top left), the unoxidized C522 lies in proximity to trimmed C...
3D-structures were downloaded from the RCSB PDB web site [28] and prepared as previously described [21]. The complexes were automatically protonated using Protoss v2.0 [29]. Importantly, water or cofactor molecules were not preserved in the protein site. In addition, all structures of the same...