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Q-SiteFinder specifications

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Unique identifier OMICS_08123
Name Q-SiteFinder
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No

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Publication for Q-SiteFinder

Q-SiteFinder citations

 (58)
library_books

Insights from the protein protein interaction network analysis of Mycobacterium tuberculosis toxin antitoxin systems

2017
Bioinformation
PMCID: 5712783
PMID: 29225431
DOI: 10.6026/97320630013380

[…] active site of vapc9 and vapc10 []. metapocket uses consensus approach to detect ligand-binding sites by employing eight methods: ligsite, pass, surfnet, fpocket, ghecom, concavity, poc asa and q-sitefinder., protein-protein association data of 79 ta systems of mtb h37rv was extracted from string v 10.5. to completely explore the ppi data, the search was set to include all the source […]

library_books

DT 13 Ameliorates TNF α Induced Vascular Endothelial Hyperpermeability via Non Muscle Myosin IIA and the Src/PI3K/Akt Signaling Pathway

2017
Front Immunol
PMCID: 5557769
PMID: 28855900
DOI: 10.3389/fimmu.2017.00925

[…] different state and sequences of the myosin models, the binding cavity was found by assistant methods based on the literature data (). the precise binding cavity was determined via ch3 probe by q-sitefinder [sp5] and blind docking by autodock3.05 [sp6]. the steps were as follows: dt-13 and homology model of nmmhc iia were prepared using ligprep and protein preparation wizard in maestro 8.0 […]

library_books

Linear epitope prediction in HPV type 16 E7 antigen and their docked interaction with human TMEM 50A structural model

2017
Bioinformation
PMCID: 5498776
PMID: 28690376
DOI: 10.6026/97320630013122

[…] with discovery studio modeler 3.5., the schrodinger software package (https://www.schrodinger .com) was used for the molecular dynamics simulation of the predicted tmem 50a model., we used q-sitefinder to locate binding site. q-sitefinder (http://www.bioinformatics.leeds.ac.uk/qsitefinder) uses the interaction energy between the protein and a simple van der waals probe to locate […]

library_books

Small molecule inhibitors block Gas6 inducible TAM activation and tumorigenicity

2017
Sci Rep
PMCID: 5341070
PMID: 28272423
DOI: 10.1038/srep43908

[…] activation., the x-ray crystal structure of the soluble gas6/axl complex (rcsb pdb entry 2c5d) was used to identify possible small molecule ligand binding sites. four independent programs: (i) the q-sitefinder, (ii) the sitemap (schrödinger suite, ny), (iii) the siteid (sybyl, tripos associates, st. louis, mo) and sitefinder (moe, ccg, montreal, canada) were used for this purpose. all ligand […]

library_books

Computational methods in drug discovery

2016
Beilstein J Org Chem
PMCID: 5238551
PMID: 28144341
DOI: 10.3762/bjoc.12.267

[…] its binding pocket, it is not necessarily true for all target proteins. energy-based methods have been developed to address this issue and have shown more success than geometry-based methods []. in q-sitefinder a van der waals probe is used and the interaction energy between the probe and the protein is found in order to identify binding sites of the protein []. the sitehound program is another […]

library_books

Improving the performance of the PLB index for ligand binding site prediction using dihedral angles and the solvent accessible surface area

2016
Sci Rep
PMCID: 5020399
PMID: 27619067
DOI: 10.1038/srep33232

[…] cavity. energy-based methods search for energetically favourably pockets for ligand binding by calculating the interaction energy between the chemical probe and protein atoms (e.g., sitehound, q-sitefinder and ftmap); in these methods, the probe can be a methyl group or atoms, such as carbon and phosphorus. sequence-based methods employ information from sequence conservation or homologous […]


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Q-SiteFinder institution(s)
School of Biochemistry and Microbiology, University of Leeds, Leeds, UK
Q-SiteFinder funding source(s)
Supported by a studentship from the BBSRC.

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