GENO3D statistics

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Citations per year

Number of citations per year for the bioinformatics software tool GENO3D
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Tool usage distribution map

This map represents all the scientific publications referring to GENO3D per scientific context
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Protocols

GENO3D specifications

Information


Unique identifier OMICS_13613
Name GENO3D
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data Protein sequence
Output data 3D models
Output format PDB
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Rhiju Das

Publication for GENO3D

GENO3D citations

 (59)
library_books

Influence of cell type and cell culture media on the propagation of foot and mouth disease virus with regard to vaccine quality

2018
Virol J
PMCID: 5857075
PMID: 29548334
DOI: 10.1186/s12985-018-0956-0

[…] Amino acid sequences of the original virus and the final passages in BHK179 and BHK-2P were used to model virus capsid protomers using the Geno3D algorithm []. The X-ray crystal structures of A24 Cruzeiro [] (Protein Data Bank accession 1ZBE) and O1 Manisa [] (1FOD) served as templates. In total, ten possible structures were generated an […]

library_books

Characterization of influenza A viruses with polymorphism in PB2 residues 701 and 702

2017
Sci Rep
PMCID: 5595998
PMID: 28900145
DOI: 10.1038/s41598-017-11625-y

[…] The structural prediction of the protein model was determined by a protein modelling tool, Geno3D, with three PDB templates (PDB ID: 3CW4, 3L56 and 2GMO). The presentation of the protein model was visualized by Chimera. The electrostatic distribution was determined by Coloumb’s Law, which i […]

library_books

An Insight Into Structure, Function, and Expression Analysis of 3 Hydroxy 3 Methylglutaryl CoA Reductase of Cymbopogon winterianus

2017
Bioinform Biol Insights
PMCID: 5390926
PMID: 28469419
DOI: 10.1177/1177932217701735

[…] able templates. To cross-check the reliability of templates identified through DELTA-BLAST program, we used fold-recognition servers for template identification which includes 3D-Jury, Pcons.net, and Geno3D. The template showing maximum identity and highest percentage of query coverage according to both fold-recognition servers and DELTA-BLAST was finally chosen for the construction of 3-dimension […]

library_books

Genomics and evolutionary aspect of calcium signaling event in calmodulin and calmodulin like proteins in plants

2017
BMC Plant Biol
PMCID: 5291997
PMID: 28158973
DOI: 10.1186/s12870-017-0989-3

[…] Molecular modeling was conducted to evaluate the molecular details of CaM and CML proteins. The Geno3d software [] was used to construct the molecular structure of CaM and CMLs. The protein sequence of AtCaM1 and AtCML1 was utilized as the query sequence to search the model. Following statistica […]

call_split

Biophysical Studies of the Induced Dimerization of Human VEGF Receptor 1 Binding Domain by Divalent Metals Competing with VEGF A

2016
PLoS One
PMCID: 5152890
PMID: 27942001
DOI: 10.1371/journal.pone.0167755
call_split See protocol

[…] . To crosscheck its validity, other models were performed by using the structure of VEGFR2d3 as template (3S37), on two other servers, CPHmodels3.2 (http://www.cbs.dtu.dk/services/CPHmodels/) [], and Geno3D (http://geno3d-pbil.ibcp.fr/) []. A fourth model was obtained from pGenThreader (http://bioinf.cs.ucl.ac.uk/psipred/) [] using the structure of VEGFR2d2d3 (2X1W). Accuracy of models was evaluat […]

call_split

Siropins, novel serine protease inhibitors from gut microbiota acting on human proteases involved in inflammatory bowel diseases

2016
Microb Cell Fact
PMCID: 5127057
PMID: 27894344
DOI: 10.1186/s12934-016-0596-2
call_split See protocol

[…] -acid sequence was done using the program ClustalW [] and the figure rendering was done using the ESPript sequence analysis server []. The 3D homology model of Siropin 1 and 2 was generated using the Geno3D server, and images were rendered by using VIEWERLITEâ„¢ 5.0. […]


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GENO3D institution(s)
Biology institute and Protein chemistry, Bioinformatics and structural NMR, Lyon, France
GENO3D funding source(s)
This work was supported by CNRS; University Lyon 1; ANRS.

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