QUARK statistics

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Citations per year

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

This map represents all the scientific publications referring to QUARK per scientific context
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Associated diseases

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Popular tool citations

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Protocols

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 citations

 (76)
library_books

In silico optimization of a guava antimicrobial peptide enables combinatorial exploration for peptide design

2018
Nat Commun
PMCID: 5902452
PMID: 29662055
DOI: 10.1038/s41467-018-03746-3

[…] 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, wh […]

library_books

Prediction of Cell Penetrating Potential of Modified Peptides Containing Natural and Chemically Modified Residues

2018
Front Microbiol
PMCID: 5906597
PMID: 29706944
DOI: 10.3389/fmicb.2018.00725

[…] g 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 modifica […]

library_books

Membrane permeabilizing amphiphilic peptide delivers recombinant transcription factor and CRISPR Cas9/Cpf1 ribonucleoproteins in hard to modify cells

2018
PLoS One
PMCID: 5884575
PMID: 29617431
DOI: 10.1371/journal.pone.0195558

[…] 1.4 2009-10-20 21:23:36 don Exp). Tridimensional representations of PTD4 and CM18 independent peptides were obtained from the following peptide prediction software: http://zhanglab.ccmb.med.umich.edu/QUARK/. Tridimensional representations of CM18-PTD4 and 6His-CM18-PTD4 peptides were obtained from the following peptide prediction software: http://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py […]

library_books

A Novel Method for Drug Screen to Regulate G Protein Coupled Receptors in the Metabolic Network of Alzheimer's Disease

2018
Biomed Res Int
PMCID: 5838471
PMID: 29675426
DOI: 10.1155/2018/5486403

[…] perimental 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, to an […]

library_books

Identification of protein W, the elusive sixth subunit of the Rhodopseudomonas palustris reaction center light harvesting 1 core complex

2018
Biochim Biophys Acta
PMCID: 5764122
PMID: 29126780
DOI: 10.1016/j.bbabio.2017.11.001

[…] t 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. […]

library_books

Biophysical insights from a single chain camelid antibody directed against the Disrupted in Schizophrenia 1 protein

2018
PLoS One
PMCID: 5764400
PMID: 29324815
DOI: 10.1371/journal.pone.0191162

[…] 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 pro […]


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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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