We get the 3D structure of protein from PDB database (https://www.rcsb.org/) and obtain corresponding 2D structure of the active ingredient from the NCBI database (https://www.ncbi.nlm.nih.gov/). Than we use SYBYL software to dock molecular structure with docking mode-Surflex-Dock Geom...
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 ...
In order to take into account the unobserved genotypes in the family 7, we followed Lauritzen and Sheehan [57] and used a Bayesian network to model the theoretical transmission of alleles in the pedigree. The model included the five bi-allelic loci of interest(DCHS1, ASTN2, CAMSAP1, GTF3C...
Protein structural domains of CDCA3 and MYC were retrieved from the Protein Data Bank (PDB; http://www.rcsb.org/). Protein-protein interactions and visualizations were analyzed using PyMOL (Version 2.4) and PDBePISA (https://www.ebi.ac.uk/pdbe/pisa/). Dual-luciferase reporter assay The CD...
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...
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...
The 3D structure of key target proteins was downloaded from the PDB database (https://www.rcsb.org). The PyMOL software was used to remove water molecules and excess inactive ligands. The AutoDockTools 1.5.6 software was imported and saved in pdbqt format. Molecular docking simulations were ...
The form of this intermolecular force is relatively homogeneous, and all of them are connected by hydrogen bonding [27, 28]. From Fig. 2A, we found that the hydrogen bonds are relatively close to the active site, which is favorable to enhance the binding tightness between the receptor ...
The crystal structures of the target proteins were obtained from the RCSB PDB database (https://www.rcsb.org/) and saved as pdbqt files. The structure of artemisinin was acquired from the PubChem database (https://pubchem.ncbi.nlm.nih.gov/) and converted into MOL2 format using Chem3D....