BSP-SLIM

[…] dentified using I-TASSER. To support the UDP-galactose binding site and to predict the binding site for inositol, low-resolution protein structures were analyzed by the blind molecular docking method BSP-SLIM []. We found that UDP-galactose and inositol are both positioned near the conserved DxD motif (A,B), which is buried deep inside the binding pocket (C,D). Furthermore, two Asp residues play a […]

[…] Pubchem databases, (CID 1983). In (SDF) format and then converted to Protein Data Bank (PDB) coordinates using the Open Babel (http://openbabel.org). Ligand binding site calculation was performed on BSP-SLIM server (http://zhanglab.ccmb.med.umich.edu/BSP-SLIM/). The modeled structure of aldehyde dehydrogenase molecule and acetaminophen were loaded on BSP-SLIM server to identify the binding pocket […]

[…] belong to solute carrier transporter family ().We next determined whether the anticancer drugs, doxorubicin and cisplatin, would dock onto the predicted structures of OCT-1 and OCT-2. We utilized the BSP-SLIM and COACH algorithms to predict the amino acid residues of the transporters constituting the ligand–protein docking sites ( and ). Since the BSP-SLIM server did not recognize the cisplatin ch […]

[…] action between TG2 and resveratrol by computational modeling using different approaches. The COACH server and TM-ALIGN analysis failed to predict the significant interaction, however, another program BSP-SLIM (for low-resolution ligand-protein docking) showed some docking positions on TG2, but it was difficult to evaluate if they indeed interact (Additional file : Figure S4a and S4b). Thus the cel […]