BSP-SLIM statistics
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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: A Blind Low-Resolution Ligand-Protein Docking Approach Using Predicted Protein Structures
BSP-SLIM citations
(4)Genome Wide Identification, Evolutionary and Expression Analyses of the GALACTINOL SYNTHASE Gene Family in Rapeseed and Tobacco
[…] 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 […]
Interaction of Aldehyde dehydrogenase with acetaminophen as examined by spectroscopies and molecular docking
[…] 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 […]
A novel approach using C. elegans DNA damage induced apoptosis to characterize the dynamics of uptake transporters for therapeutic drug discoveries
[…] 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 […]
Conformational changes and translocation of tissue transglutaminase to the plasma membranes: role in cancer cell migration
[…] 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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