QUARK protocols

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QUARK specifications

Information


Unique identifier OMICS_10835
Name QUARK
Interface Web user interface
Restrictions to use None
Input data Protein sequence
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Yang Zhang <>

Publication for QUARK

QUARK in pipelines

 (3)
2016
PMCID: 4837155
PMID: 27148198
DOI: 10.3389/fmicb.2016.00509

[…] based on the partial structure of sars-np (pdb code. 1ssk, ; pdb code. 2cjr, ) using the modeller9.15 software (). protein structures not registered in pdb were estimated by the i-tasser and quark servers and used as templates for homology modeling (; ). energy minimization of the generated model was carried out using swiss pdb viewer4.1 (). surface localization of each epitope […]

2015
PMCID: 4499774
PMID: 25826651
DOI: 10.3390/life5021141

[…] pondr (http://pondr.com) [,] as well as foldindex (http://bip.weizmann.ac.il/fldbin/findex) []. ab initio protein structure prediction for each m-repeat with flanking sequences was performed at the quark server (http://zhanglab.ccmb.med.umich.edu/quark/) [,]., the hnea csos2 gene was interrupted by inserting the kmr gene cassette into the ecorv site of csos2 (cut at nucleotide #507 in the orf […]

2013
PMCID: 3861447
PMID: 24349412
DOI: 10.1371/journal.pone.0082985

[…] were not statistically significant, most likely due to the lack of any suitable template structure in the databases to build an appropriate model. ab initio structure prediction was attempted using quark [] as no template information is required and is thus suitable for proteins with no homologues. again the results were not significant, but this is most likely due to the inherent difficulty […]


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QUARK in publications

 (45)
PMCID: 5902452
PMID: 29662055
DOI: 10.1038/s41467-018-03746-3

[…] with apd2 , for general and α-helix peptides; and phytamp for plant peptides., three-dimensional models of the 4 pg-amp1 fragments and the 15 best fitness guavanins were generated by means of quark ab initio modeling server. the models were assessed by means of prosa ii, procheck and modeller 9.17 . the stereochemical quality of a protein structure was assessed by the ramachandran plot, […]

PMCID: 5906597
PMID: 29706944
DOI: 10.3389/fmicb.2018.00725

[…] the structure of the modified peptide. in case of natural peptide user can also use following servers pep-fold (thevenet et al., ) (http://bioserv.rpbs.univ-paris-diderot.fr/services/pep-fold/) and quark (xu and zhang, ) (https://zhanglab.ccmb.med.umich.edu/quark/) for predicting structure of peptides. multiple modification options are provided there, and the user can choose the desired […]

PMCID: 5838471
PMID: 29675426
DOI: 10.1155/2018/5486403

[…] structure determination remains difficult for gpcrs []. fortunately, there are some protein 3d structure prediction methods developed for this problem, such as i-tasser [], rosetta [], and quark []. therefore, we employ the gpcr structure models predicted by gpcr-i-tasser pipeline, which is a computational method designed for 3d structure prediction of g protein-coupled receptors, […]

PMCID: 5764122
PMID: 29126780
DOI: 10.1016/j.bbabio.2017.11.001

[…] transmembrane helices (tmhs). hydrophobicity profiles were performed using the protscale/transmembrane tendency application in www.expasy.org . structural models of rpa4402 were generated using the quark and robetta servers., photosynthetic membranes were isolated from wt rps. palustris cells by rate zonal centrifugation. rc-lh1 core complexes were then purified after a further rate zonal […]

PMCID: 5764400
PMID: 29324815
DOI: 10.1371/journal.pone.0191162

[…] maps with pdb2vol, which is part of the situs package []., a starting model of the disc1691-836 protein fragment, including an n-terminal his tag, was generated by ab initio prediction using quark []. this model provided a reasonable fit to the saxs reconstruction, with a normalized spatial discrepancy (nsd) value of 1.83 as determined by supcomb []. while it yielded a very good 3d-1d […]


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QUARK institution(s)
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
QUARK funding source(s)
The NSF Career Award (DBI 1027394); the National Institute of General Medical Sciences (GM083107, GM084222)

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