BSP-SLIM

[…] 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 […]

[…] 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 […]

[…] 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 […]