GENO3D protocols

View GENO3D computational protocol

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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 in pipelines

 (4)
2017
PMCID: 5390926
PMID: 28469419
DOI: 10.1177/1177932217701735

[…] 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 […]

2013
PMCID: 3667074
PMID: 23734251
DOI: 10.1371/journal.pone.0065392

[…] used to generate a protein sequence multiple alignments with orthologs using clustal w and boxshade 3.21 (http://www.ch.embnet.org/index.html) to visualize conserved regions in the alignment. the geno3d server was used to predict secondary structure agreement to validate template selection and alignment by generating a three-dimensional structure and a model for the molecular surface […]

2013
PMCID: 3855486
PMID: 24340054
DOI: 10.1371/journal.pone.0082705

[…] searches [] and structural alignment with consurf [] were used to identify homologues of pncc. the sequences were aligned using clustalw [] and espript []. protein sequences were 3d modeled with geno3d [] and modweb []. molecular visualizations were performed with pymol (http://pymol.org) [] and chimera []. domain composition analysis of nmn deamidases was carried out using pfam database [] […]

2012
PMCID: 3339871
PMID: 22558304
DOI: 10.1371/journal.pone.0036008

[…] the protein data bank (pdb) and revealed that the ftsh from t. thermophilus (entry 2dhr), whose hexameric structure has been determined , was the closest homolog for both atftsh2 and atftsh5. the geno3d software was used for modeling the structures of atftsh2 and atftsh5. each of the hexmeric protein chains of 2dhr was used to model homo hexameric structures of both atftsh2 and atftsh5. […]


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GENO3D in publications

 (51)
PMCID: 5857075
PMID: 29548334
DOI: 10.1186/s12985-018-0956-0

[…] the passages were sequenced in arbitrary intervals., 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 […]

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

[…] to anticipate the effect of pb2-701 and 702 mutations on surface charge distributions, protein models of pb2-701 and 702 mutants (pdb id: 3cw4, 3l56 and 2gmo) were studied using automatic web server geno3d. chimera was used to predict the surface electrostatic charges of the mutants. the surface of the pb2-700 to 703 region showed a differentiated surface charge in different pb2 mutants. […]

PMCID: 5390926
PMID: 28469419
DOI: 10.1177/1177932217701735

[…] 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 […]

PMCID: 5291997
PMID: 28158973
DOI: 10.1186/s12870-017-0989-3

[…] species were named according to the orthologous genes of a. thaliana as proposed earlier [, , ]., 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 […]

PMCID: 5152890
PMID: 27942001
DOI: 10.1371/journal.pone.0167755

[…] 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 […]


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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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