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chevron_left Protein-surface structure prediction Cavity detection Tertiary structure prediction chevron_right
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EDTSurf specifications

Information


Unique identifier OMICS_16795
Name EDTSurf
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The protein structure, the specific options.
Output data The triangulated mesh surface, the atoms surrounding each cavity, the accessible surface area with respect to each residue, the depth with respect to each atom, the depth with respect to each residue.
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Yang Zhang <>

Publications for EDTSurf

EDTSurf citations

 (2)
library_books

Prediction of structural features and application to outer membrane protein identification

2015
PMCID: 4478468
PMID: 26104144
DOI: 10.1038/srep11586

[…] (rd) measures the degree of inaccessibility of a given residue buried inside a protein. the concept of rd supplements the information provided by rsa. the rd values of proteins were calculated by edtsurf program. the values output by edtsurf lie in [2.8, 9.8], where a higher value corresponds to a deeper region where a residue locate. using the same method as in ffas-3d, the rd values […]

library_books

A general and Robust Ray Casting Based Algorithm for Triangulating Surfaces at the Nanoscale

2013
PMCID: 3618509
PMID: 23577073
DOI: 10.1371/journal.pone.0059744

[…] to rotation, scale, and atom displacement. this last aspect is evidenced by cavity detection of the highly symmetric structure of fullerene, which fails when attempted by msms and has problems in edtsurf. in terms of timings, nanoshaper builds the skin surface three times faster than the single threaded version in lindow et al. on a 100,000 atoms protein and triangulates it at least ten times […]


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EDTSurf institution(s)
Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, San Diego, CA, USA; Integration Application Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
EDTSurf funding source(s)
The project is supported in part by the NSF Career Award (DBI 1027394), and the National Institute of General Medical Sciences (GM083107, GM084222).

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