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BsFinder specifications

Information


Unique identifier OMICS_21980
Name BsFinder
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A 3D structure.
Input format PDB
Output data A list of the binding sites.
Operating system Unix/Linux, Windows
Programming languages Java
Computer skills Advanced
Stability Stable
Requirements
JRE
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Lusheng Wang

Publication for BsFinder

BsFinder citations

 (3)
library_books

The PEG responding desiccome of the alder microsymbiont Frankia alni

2018
Sci Rep
PMCID: 5768760
PMID: 29335550
DOI: 10.1038/s41598-017-18839-0

[…] of the model was thus considered as satisfactory.Docking of the PEGbasic and related probes (Fig. ) was performed on this structure model. The resulting docking poses were merged and used by the SOM-BSfinder tuned version to define a 3D map of the preferential interaction spots of the PEG and its related probes with the protein surface. The resulting map and hot spots are shown in Fig. . Three po […]

library_books

Leishmania infantum 5’ Methylthioadenosine Phosphorylase presents relevant structural divergence to constitute a potential drug target

2017
BMC Struct Biol
PMCID: 5738077
PMID: 29258562
DOI: 10.1186/s12900-017-0079-7

[…] ig. 4 The protein surfaces also contained different cavities and pockets (Fig. ). In order to define and characterize the ASs and other potential BSs on the parasite protein surfaces, we used the SOM-BSfinder algorithm []. This probe-mapping method identifies potential BSs as “high neuron consensus”- areas on a 3D map. Four BSs were identified for each target (Fig. ). For huMTAP, the first site id […]

library_books

Identification of binding sites and favorable ligand binding moieties by virtual screening and self organizing map analysis

2015
BMC Bioinformatics
PMCID: 4381396
PMID: 25888251
DOI: 10.1186/s12859-015-0518-z

[…] s rates for the Top3 BSs and first BS, respectively. FTSite was tested on the same target set using the same parameter values []. It achieved 97% and 80% of success rates, respectively. We tested SOM-BSfinder with these values and obtained 97% and 88% of success for the Top3 CCs and Top1 CC, respectively. Thus, SOM-BSfinder is either as good or better than the three methods used for comparison. On […]

Citations

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BsFinder institution(s)
School of Computer Science and Technology, Shandong University, Jinan, Shandong, China; Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
BsFinder funding source(s)
Supported by a grant from the Research Grants Council of the Hong Kong Special Administrative Region, China [Project No. CityU 121608].

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