Evaluation of free modeling targets in CASP11 and ROLL

Lisa N. Kinch, Wenlin Li, Bohdan Monastyrskyy, Andriy Kryshtafovych, Nick V. Grishin

Research output: Contribution to journalArticle

40 Citations (Scopus)

Abstract

We present an assessment of 'template-free modeling' (FM) in CASP11and ROLL. Community-wide server performance suggested the use of automated scores similar to previous CASPs would provide a good system of evaluating performance, even in the absence of comprehensive manual assessment. The CASP11 FM category included several outstanding examples, including successful prediction by the Baker group of a 256-residue target (T0806-D1) that lacked sequence similarity to any existing template. The top server model prediction by Zhang's Quark, which was apparently selected and refined by several manual groups, encompassed the entire fold of target T0837-D1. Methods from the same two groups tended to dominate overall CASP11 FM and ROLL rankings. Comparison of top FM predictions with those from the previous CASP experiment revealed progress in the category, particularly reflected in high prediction accuracy for larger protein domains. FM prediction models for two cases were sufficient to provide functional insights that were otherwise not obtainable by traditional sequence analysis methods. Importantly, CASP11 abstracts revealed that alignment-based contact prediction methods brought about much of the CASP11 progress, producing both of the functionally relevant models as well as several of the other outstanding structure predictions. These methodological advances enabled de novo modeling of much larger domain structures than was previously possible and allowed prediction of functional sites.

Original languageEnglish (US)
JournalProteins: Structure, Function and Bioinformatics
DOIs
StateAccepted/In press - 2016

Fingerprint

Sequence Analysis
Servers
Proteins
Protein Domains
Experiments

Keywords

  • Ab initio
  • Alignment quality
  • CASP ROLL
  • CASP11
  • Domain structure
  • Free modeling
  • Protein fold prediction
  • Protein structure
  • Structure comparison

ASJC Scopus subject areas

  • Biochemistry
  • Structural Biology
  • Molecular Biology

Cite this

Evaluation of free modeling targets in CASP11 and ROLL. / Kinch, Lisa N.; Li, Wenlin; Monastyrskyy, Bohdan; Kryshtafovych, Andriy; Grishin, Nick V.

In: Proteins: Structure, Function and Bioinformatics, 2016.

Research output: Contribution to journalArticle

Kinch, Lisa N. ; Li, Wenlin ; Monastyrskyy, Bohdan ; Kryshtafovych, Andriy ; Grishin, Nick V. / Evaluation of free modeling targets in CASP11 and ROLL. In: Proteins: Structure, Function and Bioinformatics. 2016.
@article{5822b391d5e54285b6017188e6a91b6a,
title = "Evaluation of free modeling targets in CASP11 and ROLL",
abstract = "We present an assessment of 'template-free modeling' (FM) in CASP11and ROLL. Community-wide server performance suggested the use of automated scores similar to previous CASPs would provide a good system of evaluating performance, even in the absence of comprehensive manual assessment. The CASP11 FM category included several outstanding examples, including successful prediction by the Baker group of a 256-residue target (T0806-D1) that lacked sequence similarity to any existing template. The top server model prediction by Zhang's Quark, which was apparently selected and refined by several manual groups, encompassed the entire fold of target T0837-D1. Methods from the same two groups tended to dominate overall CASP11 FM and ROLL rankings. Comparison of top FM predictions with those from the previous CASP experiment revealed progress in the category, particularly reflected in high prediction accuracy for larger protein domains. FM prediction models for two cases were sufficient to provide functional insights that were otherwise not obtainable by traditional sequence analysis methods. Importantly, CASP11 abstracts revealed that alignment-based contact prediction methods brought about much of the CASP11 progress, producing both of the functionally relevant models as well as several of the other outstanding structure predictions. These methodological advances enabled de novo modeling of much larger domain structures than was previously possible and allowed prediction of functional sites.",
keywords = "Ab initio, Alignment quality, CASP ROLL, CASP11, Domain structure, Free modeling, Protein fold prediction, Protein structure, Structure comparison",
author = "Kinch, {Lisa N.} and Wenlin Li and Bohdan Monastyrskyy and Andriy Kryshtafovych and Grishin, {Nick V.}",
year = "2016",
doi = "10.1002/prot.24973",
language = "English (US)",
journal = "Proteins: Structure, Function and Bioinformatics",
issn = "0887-3585",
publisher = "Wiley-Liss Inc.",

}

TY - JOUR

T1 - Evaluation of free modeling targets in CASP11 and ROLL

AU - Kinch, Lisa N.

AU - Li, Wenlin

AU - Monastyrskyy, Bohdan

AU - Kryshtafovych, Andriy

AU - Grishin, Nick V.

PY - 2016

Y1 - 2016

N2 - We present an assessment of 'template-free modeling' (FM) in CASP11and ROLL. Community-wide server performance suggested the use of automated scores similar to previous CASPs would provide a good system of evaluating performance, even in the absence of comprehensive manual assessment. The CASP11 FM category included several outstanding examples, including successful prediction by the Baker group of a 256-residue target (T0806-D1) that lacked sequence similarity to any existing template. The top server model prediction by Zhang's Quark, which was apparently selected and refined by several manual groups, encompassed the entire fold of target T0837-D1. Methods from the same two groups tended to dominate overall CASP11 FM and ROLL rankings. Comparison of top FM predictions with those from the previous CASP experiment revealed progress in the category, particularly reflected in high prediction accuracy for larger protein domains. FM prediction models for two cases were sufficient to provide functional insights that were otherwise not obtainable by traditional sequence analysis methods. Importantly, CASP11 abstracts revealed that alignment-based contact prediction methods brought about much of the CASP11 progress, producing both of the functionally relevant models as well as several of the other outstanding structure predictions. These methodological advances enabled de novo modeling of much larger domain structures than was previously possible and allowed prediction of functional sites.

AB - We present an assessment of 'template-free modeling' (FM) in CASP11and ROLL. Community-wide server performance suggested the use of automated scores similar to previous CASPs would provide a good system of evaluating performance, even in the absence of comprehensive manual assessment. The CASP11 FM category included several outstanding examples, including successful prediction by the Baker group of a 256-residue target (T0806-D1) that lacked sequence similarity to any existing template. The top server model prediction by Zhang's Quark, which was apparently selected and refined by several manual groups, encompassed the entire fold of target T0837-D1. Methods from the same two groups tended to dominate overall CASP11 FM and ROLL rankings. Comparison of top FM predictions with those from the previous CASP experiment revealed progress in the category, particularly reflected in high prediction accuracy for larger protein domains. FM prediction models for two cases were sufficient to provide functional insights that were otherwise not obtainable by traditional sequence analysis methods. Importantly, CASP11 abstracts revealed that alignment-based contact prediction methods brought about much of the CASP11 progress, producing both of the functionally relevant models as well as several of the other outstanding structure predictions. These methodological advances enabled de novo modeling of much larger domain structures than was previously possible and allowed prediction of functional sites.

KW - Ab initio

KW - Alignment quality

KW - CASP ROLL

KW - CASP11

KW - Domain structure

KW - Free modeling

KW - Protein fold prediction

KW - Protein structure

KW - Structure comparison

UR - http://www.scopus.com/inward/record.url?scp=84955311378&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84955311378&partnerID=8YFLogxK

U2 - 10.1002/prot.24973

DO - 10.1002/prot.24973

M3 - Article

C2 - 26677002

AN - SCOPUS:84955311378

JO - Proteins: Structure, Function and Bioinformatics

JF - Proteins: Structure, Function and Bioinformatics

SN - 0887-3585

ER -