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Information


Unique identifier OMICS_08132
Name eFindSite
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.2
Stability Stable
Maintained No

Versioning


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Maintainer


This tool is not maintained anymore.

Information


Unique identifier OMICS_08132
Name eFindSite
Interface Web user interface
Restrictions to use Academic or non-commercial use
Computer skills Basic
Version 1.2
Stability Stable
Maintained No

Maintainer


This tool is not maintained anymore.

Publication for eFindSite

eFindSite citations

 (5)
call_split

Determination of genotypic and clinical characteristics of Colombian patients with mucopolysaccharidosis IVA

2018
PMCID: 5926073
PMID: 29731656
DOI: 10.2147/TACG.S141881
call_split See protocol

[…] wild-type structure of GALNS code 4FDI (due to its 2.2 Å resolution) using the SWISS-model platform. The X, Y, and Z coordinates to be used in AutoDock Tools (version 1.5.6) were calculated with the eFindsite platform (http://brylinski.cct.lsu.edu/efindsite; Louisiana State University). Calculations led to seven options for pocket coordinates, and the authors selected the one with the best confid […]

library_books

Large scale computational drug repositioning to find treatments for rare diseases

2018
NPJ Syst Biol Appl
PMCID: 5847522
PMID: 29560273
DOI: 10.1038/s41540-018-0050-7

[…] Target structures composed of 50–999 amino acids in both datasets were modeled with eThread, a template-based structure prediction algorithm. In the next step, drug-binding pockets were predicted by eFindSite in confidently modeled target DrugBank and Orphanet proteins whose estimated GDT-score is ≥0.4. Drug repositioning utilizes only those binding sites assigned a high and moderate confidence. […]

library_books

Molecular Cloning of HbPR 1 Gene from Rubber Tree, Expression of HbPR 1 Gene in Nicotiana benthamiana and Its Inhibition of Phytophthora palmivora

2016
PLoS One
PMCID: 4940168
PMID: 27337148
DOI: 10.1371/journal.pone.0157591

[…] His121 and Cys142 within α-helix H1 and H3 were possibly bound to EAH molecule (). To further analyze HbPR-1 structure in details, we have predicted the protein-protein interaction sites by using the eFindSite server. The eFindSite prediction result suggested that HbPR-1 had a high confidential score of protein-protein binding with the thirteen interfacial residues: Asn70, Val72-Asn76, Gln118, Gly […]

call_split

Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets

2015
J Cheminform
PMCID: 4468813
PMID: 26082804
DOI: 10.1186/s13321-015-0067-5
call_split See protocol

[…] entative complex structures included in DUD-E (the D101 set). Furthermore, we evaluate the accuracy of virtual screening for a subset of 77 proteins whose binding sites were successfully predicted by eFindSite (the D77 set). A binding site prediction is considered successful when the distance between the predicted and experimental pocket center is below 8 Å. […]

library_books

A Sialoreceptor Binding Motif in the Mycoplasma synoviae Adhesin VlhA

2014
PLoS One
PMCID: 4206340
PMID: 25338071
DOI: 10.1371/journal.pone.0110360

[…] were predicted to be highly destabilizing. The potential to bind sialic acid (KEGG Compound C00270; PubChem.sdf 445063) or any other ligand in the KEGG Compound database was predicted by applying the eFindSite ligand binding site prediction algorithm (http://brylinski.cct.lsu.edu/) – also to the.pdb files generated by Phyre2. […]

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eFindSite institution(s)
Center for Computation & Technology, Louisiana State University, Baton Rouge, LA, USA

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