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BSP-SLIM specifications

Information


Unique identifier OMICS_10800
Name BSP-SLIM
Interface Web user interface
Restrictions to use None
Input data Receptor structure (PDB format) and ligand structure (SDF format)
Input format PDB, SDF
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Yang Zhang <>

Publication for BSP-SLIM

BSP-SLIM in publications

 (3)
PMCID: 5751367
PMID: 29261107
DOI: 10.3390/ijms18122768

[…] 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 […]

PMCID: 5614660
PMID: 28955748
DOI: 10.1016/j.bbrep.2017.03.010

[…] 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 […]

PMCID: 5081529
PMID: 27786254
DOI: 10.1038/srep36026

[…] 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 […]


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BSP-SLIM institution(s)
Center for Computational Medicine and Bioinformatics, Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
BSP-SLIM funding source(s)
The project is supported in part by the NSF Career Award (DBI 0746198), and National Institute of General Medical Sciences (GM083107, GM084222).

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