SiteMap protocols

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SiteMap specifications

Information


Unique identifier OMICS_18932
Name SiteMap
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Thomas Halgren <>

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Publications for SiteMap

SiteMap in pipeline

2014
PMCID: 4263601
PMID: 25501935
DOI: 10.1371/journal.pone.0114131

[…] were processed with ligprep . the processing ensured proper bond orders and, using the epik , module, generated all possible tautomers of the ligands to reflect a ph in the range of 5.0 to 9.0. sitemap , software was used to probe the surface of the tβr-1 for possible binding pockets. a total of five binding pockets were identified; these were ranked based on characteristics that included […]


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SiteMap in publications

 (27)
PMCID: 5909492
PMID: 29706972
DOI: 10.3389/fpls.2018.00344

[…] medium resolution were created using the 1.0 scaling factor for the van der waals radius and a rolled probe radius of 1.4 å. assessment of nfr5 protein active sites was conducted by the schrödinger sitemap application (halgren, ). based on the collection of nfr5 models, we assessed the matrix of frequencies that two amino acids placed in one active site, {mi,j}:, where nm is the number […]

PMCID: 5817085
PMID: 29492402
DOI: 10.3389/fchem.2018.00023

[…] predictions were performed using tmbase (hofmann and stoffel, ) and gpcrhmm server (wistrand et al., ). tmbase and gprcrhmm algorithm were based on statistical and hmm analysis, respectively., sitemap module of schrödinger software suite (halgren, , ) was used to predict the binding site of gpr142. sitemap used the interaction energies to locate the energetically favorable regions. […]

PMCID: 5663397
PMID: 29088253
DOI: 10.1371/journal.pone.0186869

[…] in ectosteric site 1, a molecular docking approach was used. we first investigated the druggability of this site by analyzing the molecular surface and performing computational analysis using sitemap (schrödinger inc.)., the binding pocket of ectosteric site 1 consists mostly of negatively charged surface residues with tyr87 forming the hydrophobic interior of the pocket and residues […]

PMCID: 5669120
PMID: 29142437
DOI: 10.4103/pm.pm_49_17

[…] the schrödinger software suite with default parameters and proteins were prepared using the protein preparation wizard. receptor grid was prepared with default parameters without any constraints.[] sitemap was used for prediction and evaluation of binding sites.[] the emodel and glide scores were used to predict the binding affinity of docked structures using the sp and xp feature of glide […]

PMCID: 5500575
PMID: 28684785
DOI: 10.1038/s41598-017-05058-w

[…] matches involving more sites. hits were sorted by fitness score and clustered with canvas to select diverse representative structures. as a secondary assessment of compound structures, we used sitemap on a h3 structure model. after the first assaying round small structure-activity relationship analyses were conducted and the compounds sorted into lead ligand series. the selections […]


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