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Protocols

eF-site specifications

Information


Unique identifier OMICS_22549
Name eF-site
Alternative name electrostatic surface of Functional-site
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Haruki kamura

Publications for electrostatic surface of Functional-site

eF-site citations

 (16)
library_books

New tools and functions in data‐out activities at Protein Data Bank Japan (PDBj)

2017
PMCID: 5734392
PMID: 28815765
DOI: 10.1002/pro.3273

[…] owing the protein dynamics using the all‐atom normal mode analysis (NMA), ProMode‐Elastic. Fourth, we show a virtual reality (VR) application for the database of the electrostatic molecular surfaces, eF‐site, for educational purposes. Fifth, we introduce the extension of molecular shape comparison server, Omokage search, where searching for the Small Angle Scattering Biological Data Bank (SASBDB) […]

call_split

Crystal structure of the N myristoylated lipopeptide bound MHC class I complex

2016
Nat Commun
PMCID: 4735555
PMID: 26758274
DOI: 10.1038/ncomms10356
call_split See protocol

[…] and HLA-Cw4 (1QQD) (). The VDW forces were estimated by a fragment molecular orbital calculation using the PAICS programme (). Electrostatic potential was calculated using the eF-surf server (http://ef-site.hgc.jp/eF-surf/; ). […]

library_books

Exhaustive comparison and classification of ligand binding surfaces in proteins

2013
PMCID: 3795496
PMID: 23934772
DOI: 10.1002/pro.2329

[…] h method for comparing a huge number of patches, by applying a hash table. Patches, except for DNA, RNA, monoatomic ions, and unknown ligands, were extracted from molecular surface data stored at the eF-site. We prepared representative patches by performing hierarchical clustering for patches with the same three letter code of the PDB chemical component identifier (Ligand ID), using patch similari […]

library_books

Design of a Modular Protein Based MRI Contrast Agent for Targeted Application

2013
PLoS One
PMCID: 3675113
PMID: 23762349
DOI: 10.1371/journal.pone.0065346

[…] properties according to the HSAB concept. Terbium(III), however, shows detectable luminescence upon binding to a chelating compound. Therefore, the affinity for complex formation of the high affinity EF-site of Zarvin and Tb3+ was estimated first in a competition assay using nitrilotriacetic acid (NTA) as a competitor. Using the fitted apparent affinity of NTA:Tb3+ and the binding affinity of 5.6 […]

library_books

Rapid Catalytic Template Searching as an Enzyme Function Prediction Procedure

2013
PLoS One
PMCID: 3651201
PMID: 23675414
DOI: 10.1371/journal.pone.0062535

[…] ify enzymatic sites with SPASM . Other groups have used graph searching procedures, with specialized atom typing, such as Cavbase , PINTS , , and Query3D , or surface features as descriptors, such as eF-site , SuMo , and SiteEngine , whereby complex and physically motivated descriptors are used as nodes for the graph comparisons.Other approaches to the template matching problem use a procedure kno […]

library_books

Efficient protein structure search using indexing methods

2013
BMC Med Inform Decis Mak
PMCID: 3618241
PMID: 23691543
DOI: 10.1186/1472-6947-13-S1-S8

[…] lassification. Some database systems that are able to take a query structure are for the search includes Distance matrix ALIgnment (DALI) server [], Vector Alignment Search Tool (VAST) search [], and eF-site database []. Given a query protein structure, they need around an hour to finish searching their databases. Zeyar et al. suggests an indexing method called ProtDex for fast search in 3D protei […]

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eF-site institution(s)
Graduate School of Integrated Science, Yokohama City University, Yokohama, Japan; Structure and Function of Biomolecules, PRESTO, JST, Saitama, Japan; Institute for Protein Research, Osaka University, Osaka, Japan
eF-site funding source(s)
Supported by a grant-in-aid from Institute for Bioinformatics Research and Development, Japan Science and Technology Agency (BIRD-JST).

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