3D-Jury protocols

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3D-Jury specifications

Information


Unique identifier OMICS_14999
Name 3D-Jury
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data An amino acid sequence.
Computer skills Basic
Stability No
Maintained No

Maintainer


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Publication for 3D-Jury

3D-Jury in pipelines

 (7)
2017
PMCID: 5390926
PMID: 28469419
DOI: 10.1177/1177932217701735

[…] to select the suitable 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 […]

2007
PMCID: 2048972
PMID: 17877795
DOI: 10.1186/1471-2105-8-345

[…] comparison of multiple models or additional information from multiple servers; all other methods are capable of producing a single score based on a single model., the top models selected using the 3d-jury method are shown to be of significantly higher quality (p < 0.01) than those selected using any other method according to the tm-score, maxsub score and gdt score. the top models selected […]

2007
PMCID: 2048972
PMID: 17877795
DOI: 10.1186/1471-2105-8-345

[…] for each target separately and then the mean overall rho value is taken. it is clear that the ordering of methods has changed and this was also shown to occur in the official assessment. the 3d-jury method and the lee method are still ranked as the top performing methods but there is a re-ordering of the other methods. contrary to the results shown in table , it would appear […]

2006
PMCID: 1635247
PMID: 16971460
DOI: 10.1093/nar/gkl480

[…] of 10−3 and within 10−15 of the top hit for psi-blast detections, at least −8.0 and within 12.0 of the top confidence hit for ffas03 detections, and at least 20.0 and within 30.0 of the top hit for 3d-jury detections), we found that the best possible parent (as measured by the mammoth maxsub quality of the best 3d-pair () structural alignment derived template) on average increased from 70.6 […]

2006
PMCID: 1635247
PMID: 16971460
DOI: 10.1093/nar/gkl480

[…] the best parent. only for a few of the most challenging targets does the initial k*sync ensemble not manage to sample near the best possible alignment. we find that for 21 of the 27 targets in the 3d-jury regime, the k*sync ensemble achieves at least one model of quality close to that of the model produced by the 3d-pair alignment to the best parent (within ∼10% of the full query length […]


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3D-Jury in publications

 (65)
PMCID: 5390926
PMID: 28469419
DOI: 10.1177/1177932217701735

[…] to select the suitable 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 […]

PMCID: 5172416
PMID: 15629054
DOI: 10.1016/S1672-0229(03)01031-3

[…] fold with a cys-his at the active site was recognized. on the other hand, the modeling of the structure of 20-o-mt domain located at nsp16 was proposed by von grotthuss et al using the 3d jury system with high reliability (3d jury score >100). the conservation of the unique tetrad residues k-d-k-e of the domain assigned a proposed mrna cap methylation function of this domain, […]

PMCID: 4857005
PMID: 27060136
DOI: 10.1093/nar/gkw222

[…] after manually curated superposition of their structures. secondary structures were assigned with dssp ()., potential templates were identified with meta-basic and the consensus of fold recognition 3d-jury approach () using human fam46 proteins as queries. the sequence-to-structure alignment between fam46 family members and all representative structures possessing both ntase and pap/oas1 sbd […]

PMCID: 4813553
PMID: 26797119
DOI: 10.1074/jbc.M115.683888

[…] software suite () to generate models of protein domains by automatically combining template-based homology modeling and de novo approaches. it first screens the sequence using blast, psi-blast, and 3d-jury for regions that possess a homolog with an experimentally determined structure and then parses the sequence into putative domains on the basis of matches to both known and predicted […]

PMCID: 4575145
PMID: 26384328
DOI: 10.1371/journal.pone.0138034

[…] 3.1.1) as it possesses a nucleophile-his-acid catalytic triad characteristic of typical carboxylic ester hydrolase []. an α/β-hydrolase fold protein was first time described by ollis et al. []. the 3d-jury structure based analysis using bioinfometaserver revealed that the hypothetical protein daci_4366 has structural similarity with different ntn-hydrolases. inspection of genome database […]


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3D-Jury institution(s)
BioInfoBank Institute, Poznan, Poland; Stockholm Bioinformatics Center, AlbaNova, Stockholm University, Stockholm, Sweden; Bioinformatics, Department of Computer Science, Beer-Sheva, Israel

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