ESyPred3D protocols

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ESyPred3D specifications

Information


Unique identifier OMICS_10526
Name ESyPred3D
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 1.0
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/ESyPred3D

Maintainer


  • person_outline Christophe Lambert <>

Publication for ESyPred3D

ESyPred3D in pipelines

 (6)
2015
PMCID: 4527572
PMID: 26261417
DOI: 10.2147/IJN.S77675

[…] did not find any available database for it). these pdb templates were selected on the basis of high score, maximum percentage identity, and low e-value. chitinase and jacob were modeled through the esypred3d program. the esypred3d program is an automated homology modeling program based on an artificial neural networks computational model. final models were visualized by pymol viewer., […]

2014
PMCID: 4142287
PMID: 25180173
DOI: 10.1155/2014/850607

[…] []. t. indiensis trx showed 29% sequence similarity (92% query coverage) with t. scotoductus trx and 24% sequence similarity (95% query coverage) with m. gryphiswaldense fer5 by blast analysis (). esypred3d program predicted the 3d structures of t. indiensis trx and m. gryphiswaldense fer5 by using escherichia coli thioredoxin reductase crystal structure (pdb id 1cl0) as the template […]

2014
PMCID: 4142287
PMID: 25180173
DOI: 10.1155/2014/850607

[…] reductase (tdr) (). blast analysis found high sequence similarity of t. indiensis tdr with t. scotoductus trx and m. gryphiswaldense fer5 (). the 3d structure of t. indiensis tdr was predicted by esypred3d using mycobacterium tuberculosis thioredoxin reductase crystal structure (pdb id 2a87) as the template (). 3d structural alignment of t. indiensis tdr against t. scotoductus trx and m. […]

2013
PMCID: 4017273
PMID: 23869567
DOI: 10.1080/07391102.2013.818576

[…] were unable to capture any possible template for modeling athk1 sensory domain sequence. hence, the athk1 sensory domain sequence was modeled using threading approach using cphmodels server () and esypred3d (), while chase domain of oshk3b was modeled using comparative modeling approach (see method) (supplementary ). the results obtained from cph webserver and esypred3d consensually identified […]

2012
PMCID: 3517979
PMID: 23230516
DOI: 10.1038/srep00951

[…] conditions., for trypan blue staining, infected leaves were stained with 0.05% trypan blue for 45 min and washed with pbs. all samples were viewed under light microscopy at 40× magnification., esypred3d server was used for comparative homology modelling and i-tasser loop prediction server was used for threading. quality of model was checked by procheck analysis. ched server was used […]

ESyPred3D in publications

 (53)
PMCID: 5633885
PMID: 29017516
DOI: 10.1186/s13071-017-2379-y

[…] not been resolved experimentally, we used a virtual structural model based on its homology with human akt1 protein, previously reported in the protein data bank (pdb). the model was built using the esypred3d web server 1.0 program []. the structure of the akt inhibitor x was obtained from zinc database [] in mol2 format. to improve the modeling of the putative interaction between protein […]

PMCID: 5668010
PMID: 29108277
DOI: 10.18632/oncotarget.20694

[…] by the p.g155d mutation is highly conserved between primate mammal species (figure ). the three dimensional structure of the cabp4 protein with the novel missense mutation was modeled using the esypred3d web server (figure ). the c.464g>a substitution replaces a glycine residue with an aspartic acid residue, additionally containing an acidic side chain, at position 155, which is within […]

PMCID: 5417653
PMID: 28472157
DOI: 10.1371/journal.pone.0177090

[…] correlations and conservation were calculated using pfstats as described previously []., molecular modeling of rtg2p was performed in five independent servers, robetta [], swiss-model [], phyre2 [], esypred3d [] and i-tasser [] using default settings. the models obtained were validated by analysis of the ramachandran diagram () and through verify3d program () []. the best model showed 90.2% […]

PMCID: 5348726
PMID: 28326224
DOI: 10.1038/boneres.2017.3

[…] mapkkk family, and play a critical role in regulating osteoclast differentiation and bone formation., we have chosen tak1 as a template to build three-dimensional structures of human lrrk1 using the esypred3d automated homology modeling program (swiss institute of bioinformatics, switzerland) because mice with disruption of tak1 also show an osteopetrosis phenotype., sequence analyses […]

PMCID: 5288522
PMID: 28197415
DOI: 10.1155/2017/5925714

[…] homology modeling was employed to predict three-dimensional (3d) structures of daoa by satisfying spatial restraints. threading approach (swiss model [], i-tasser [], mod-web [], 3d-jigsaw [], and esypred3d []) were also employed for structure prediction. the 3d structures for daoa isoforms were visualized on ucsf chimera 1.10. the predicted structures of daoa isoforms were minimized by amber […]

ESyPred3D institution(s)
Facultés Universitaires Notre-Dame de la Paix, Unité de Recherche en Biologie Moléculaire, Namur, Belgium

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