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3DLigandSite specifications

Information


Unique identifier OMICS_03794
Name 3DLigandSite
Interface Web user interface
Restrictions to use None
Input data A protein sequence or a structure.
Output data Details of the phyre model used (only where a sequence has been submitted) and details of the search against the structural library, a table of the ligand clusters identified and the 3DLigandSite prediction.
Computer skills Basic
Stability Stable
Maintained No

Maintainer


This tool is not available anymore.

Publication for 3DLigandSite

3DLigandSite in publications

 (67)
PMCID: 5964351
DOI: 10.1128/mBio.00869-18

[…] from hunovs for either of the bat virus sequences. the btcalv/a10 dimer () and btnov dimer () each resembled the p dimers of their hunov counterparts (). additionally, the open source software 3dligandsite () indicated that the models retained ligand binding sites (red) for type a hbgas (white spheres) similar to those seen with the gii.4 hunov backbone., as we had shown that btnov vlps […]

PMCID: 5871713
PMID: 29618982
DOI: 10.3389/fphys.2018.00252

[…] (http://www.cbs.dtu.dk/services/signalp) and euk-mploc 2.0 (http://www.csbio.sjtu.edu.cn/bioinf/euk-multi-2/) were applied to predict signal peptides and subcellular localization, respectively. the 3dligandsite tool (http://www.sbg.bio.ic.ac.uk/3dligandsite) was utilized to predict ligand-binding sites in the proteins. the phyre2 tool (http://www.sbg.bio.ic.ac.uk/$\sim$phyre2/) was employed […]

PMCID: 5730167
PMID: 29240782
DOI: 10.1371/journal.pone.0189303

[…] techniques for a remote homology detection. the protein model generated by the phyre2 was used to predict the ligand-binding sites by the 3d ligand site software? (http://www.sbg.bio.ic.ac.uk/3dligandsite;). the 3d ligand site predicted binding sites based on the comparison of query structure with a binding site library, which is extracted from protein–ligand complexes, to select similar […]

PMCID: 5703496
PMID: 29176870
DOI: 10.1371/journal.pone.0187793

[…] plot analysis of the ecmdar 3d model was done by ramepage web server (http://mordred.bioc.cam.ac.uk/~rapper/rampage). active site and ligand binding site prediction of ecmdar was done by 3dligandsite (www.sbg.bio.ic.ac.uk/3dligandsite). a gene to gene interaction analysis for ecmdar was done through string based analysis (http://string-db.org). the promoter prediction tool 2.0 […]

PMCID: 5648872
PMID: 29051512
DOI: 10.1038/s41598-017-12881-8

[…] regarding cd300b receptor crystal structure, we decided to address this question by means of bioinformatic prediction tools. we submitted the human cd300b immunoglobulin (ig) domain sequence to the 3dligandsite web server (http://www.sbg.bio.ic.ac.uk/3dligandsite). the server predicts first a protein structure using protein homology/analogy recognition engine (phyre), which is then used […]


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3DLigandSite institution(s)
Structural Bioinformatics Group, Centre for Bioinformatics, Imperial College London, London, UK
3DLigandSite funding source(s)
Biotechnology and Biological Sciences Research Council (grants BB/F020481/1 BB/E000940/1).

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