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Protocols

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 citations

 (4)
library_books

Genome Wide Identification, Evolutionary and Expression Analyses of the GALACTINOL SYNTHASE Gene Family in Rapeseed and Tobacco

2017
Int J Mol Sci
PMCID: 5751367
PMID: 29261107
DOI: 10.3390/ijms18122768

[…] 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 […]

call_split

Interaction of Aldehyde dehydrogenase with acetaminophen as examined by spectroscopies and molecular docking

2017
PMCID: 5614660
PMID: 28955748
DOI: 10.1016/j.bbrep.2017.03.010
call_split See protocol

[…] 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 […]

call_split

A novel approach using C. elegans DNA damage induced apoptosis to characterize the dynamics of uptake transporters for therapeutic drug discoveries

2016
Sci Rep
PMCID: 5081529
PMID: 27786254
DOI: 10.1038/srep36026
call_split See protocol

[…] 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 […]

library_books

Conformational changes and translocation of tissue transglutaminase to the plasma membranes: role in cancer cell migration

2014
BMC Cancer
PMCID: 4021189
PMID: 24725450
DOI: 10.1186/1471-2407-14-256

[…] 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 […]

Citations

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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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