SURFNET protocols

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SURFNET specifications

Information


Unique identifier OMICS_08122
Name SURFNET
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for SURFNET

SURFNET in pipeline

2017
PMCID: 5620967
PMID: 28979936
DOI: 10.1021/acscentsci.7b00211

[…] binding pockets in static structures., some of these rely on the voronoi diagrams (e.g., molaxis, mole), grids (e.g., pocket, pocketfinder, povme,), and molecular surfaces and probes (e.g., hole, surfnet). other algorithms analyze ensembles of structures, but usually require a preliminary structural alignment (e.g., mdpocket, pocketanalizerpca, epock, trj_cavity, and trapp). in this case, […]


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SURFNET in publications

 (55)
PMCID: 5929906
PMID: 29712619
DOI: 10.7554/eLife.32271.037

[…] active, ‘in’ position, lapatinib binding results in a potential steric clash with her2e770/m774 (). a general decrease of the nucleotide binding pocket volume from 756 å3 to 232 å3 (calculated using surfnet v1.5 ()) supports these predictions., to further test whether the lapatinib-induced her2-her3 is adopting the canonical activator/receiver orientation, we used fret-flim to investigate […]

PMCID: 5712783
PMID: 29225431
DOI: 10.6026/97320630013380

[…] quality., metapocket 2.0 was employed to determine 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, […]

PMCID: 5620967
PMID: 28979936
DOI: 10.1021/acscentsci.7b00211

[…] binding pockets in static structures., some of these rely on the voronoi diagrams (e.g., molaxis, mole), grids (e.g., pocket, pocketfinder, povme,), and molecular surfaces and probes (e.g., hole, surfnet). other algorithms analyze ensembles of structures, but usually require a preliminary structural alignment (e.g., mdpocket, pocketanalizerpca, epock, trj_cavity, and trapp). in this case, […]

PMCID: 5434337
PMID: 28498943
DOI: 10.1093/cid/cix169

[…] no.:hhsn272200900018c, grant no. u19ai110818 to the broad institute]. this research used infrastructure resources from the broad institute, the delft university of technology, internet2, and surfnet (the dutch research and education network), supported under the enlighten your research global program., ethics statement. informed consent was obtained. the study protocol was approved […]

PMCID: 5325476
PMID: 28234935
DOI: 10.1371/journal.pone.0172217

[…] by using meta pocket 2.0 (mpk2) web tool []. this server utilizes a consensus method in which the binding sites are predicted by eight different methods including ligsitecs, pass, q-site finder, surfnet, fpocket, ghecom, con-cavity and pocasa. indeed, several tools were applied to improve the accuracy of identification of putative binding pockets. taken together, it was found […]


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SURFNET institution(s)
Department of Biochemistry and Molecular Biology, University College, London, UK

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