Applying Undertaker to quality assessment

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Applying Undertaker to quality assessment. / Archie, John G.; Paluszewski, Martin; Karplus, Kevin.

In: Proteins - Structure Function and Bioinformatics, Vol. 77, No. S9, 2009, p. 191-195.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Archie, JG, Paluszewski, M & Karplus, K 2009, 'Applying Undertaker to quality assessment', Proteins - Structure Function and Bioinformatics, vol. 77, no. S9, pp. 191-195. https://doi.org/10.1002/prot.22508

APA

Archie, J. G., Paluszewski, M., & Karplus, K. (2009). Applying Undertaker to quality assessment. Proteins - Structure Function and Bioinformatics, 77(S9), 191-195. https://doi.org/10.1002/prot.22508

Vancouver

Archie JG, Paluszewski M, Karplus K. Applying Undertaker to quality assessment. Proteins - Structure Function and Bioinformatics. 2009;77(S9):191-195. https://doi.org/10.1002/prot.22508

Author

Archie, John G. ; Paluszewski, Martin ; Karplus, Kevin. / Applying Undertaker to quality assessment. In: Proteins - Structure Function and Bioinformatics. 2009 ; Vol. 77, No. S9. pp. 191-195.

Bibtex

@article{2e8151a0172511df8ed1000ea68e967b,
title = "Applying Undertaker to quality assessment",
abstract = "Our group tested three quality assessment functions in CASP8: a function which used only distance constraints derived from alignments (SAM-T08-MQAO), a function which added other single-model terms to the distance constraints (SAM-T08-MQAU), and a function which used both single-model and consensus terms (SAM-T08-MQAC). We analyzed the functions both for ranking models for a single target and for producing an accurate estimate of GDT_TS. Our functions were optimized for the ranking problem, so are perhaps more appropriate for metaserver applications than for providing trustworthiness estimates for single models. On the CASP8 test, the functions with more terms performed better. The MQAC consensus method was substantially better than either single-model function, and the MQAU function was substantially better than the MQAO function that used only constraints from alignments. Proteins 2009. {\textcopyright} 2009 Wiley-Liss, Inc.",
author = "Archie, {John G.} and Martin Paluszewski and Kevin Karplus",
note = "Keywords Undertaker • quality assessment • CASP • metaserver",
year = "2009",
doi = "10.1002/prot.22508",
language = "English",
volume = "77",
pages = "191--195",
journal = "Proteins: Structure, Function, and Bioinformatics",
issn = "0887-3585",
publisher = "JohnWiley & Sons, Inc.",
number = "S9",

}

RIS

TY - JOUR

T1 - Applying Undertaker to quality assessment

AU - Archie, John G.

AU - Paluszewski, Martin

AU - Karplus, Kevin

N1 - Keywords Undertaker • quality assessment • CASP • metaserver

PY - 2009

Y1 - 2009

N2 - Our group tested three quality assessment functions in CASP8: a function which used only distance constraints derived from alignments (SAM-T08-MQAO), a function which added other single-model terms to the distance constraints (SAM-T08-MQAU), and a function which used both single-model and consensus terms (SAM-T08-MQAC). We analyzed the functions both for ranking models for a single target and for producing an accurate estimate of GDT_TS. Our functions were optimized for the ranking problem, so are perhaps more appropriate for metaserver applications than for providing trustworthiness estimates for single models. On the CASP8 test, the functions with more terms performed better. The MQAC consensus method was substantially better than either single-model function, and the MQAU function was substantially better than the MQAO function that used only constraints from alignments. Proteins 2009. © 2009 Wiley-Liss, Inc.

AB - Our group tested three quality assessment functions in CASP8: a function which used only distance constraints derived from alignments (SAM-T08-MQAO), a function which added other single-model terms to the distance constraints (SAM-T08-MQAU), and a function which used both single-model and consensus terms (SAM-T08-MQAC). We analyzed the functions both for ranking models for a single target and for producing an accurate estimate of GDT_TS. Our functions were optimized for the ranking problem, so are perhaps more appropriate for metaserver applications than for providing trustworthiness estimates for single models. On the CASP8 test, the functions with more terms performed better. The MQAC consensus method was substantially better than either single-model function, and the MQAU function was substantially better than the MQAO function that used only constraints from alignments. Proteins 2009. © 2009 Wiley-Liss, Inc.

U2 - 10.1002/prot.22508

DO - 10.1002/prot.22508

M3 - Journal article

C2 - 19639637

VL - 77

SP - 191

EP - 195

JO - Proteins: Structure, Function, and Bioinformatics

JF - Proteins: Structure, Function, and Bioinformatics

SN - 0887-3585

IS - S9

ER -

ID: 17558355