CASP5 Target Classification

Lisa N. Kinch, Yuan Qi, Tim J P Hubbard, Nick V. Grishin

Research output: Contribution to journalArticle

22 Citations (Scopus)

Abstract

This report summarizes the Critical Assessment of Protein Structure Prediction (CASP5) target proteins, which included 67 experimental models submitted from various structural genomics efforts and independent research groups. Throughout this special issue, CASP5 targets are referred to with the identification numbers T0129-T0195. Several of these targets were excluded from the assessment for various reasons: T0164 and T0166 were cancelled by the organizers; T0131, T0144, T0158, T0163, T0171, T0175, and T0180 were not available in time; T0145 was "natively unfolded"; the T0139 structure became available before the target expired; and T0194 was solved for a different sequence than the one submitted. Table I outlines the sequence and structural information available for CASP5 proteins in the context of existing folds and evolutionary relationships. This information provided the basis for a domain-based classification of the target structures into three assessment categories: comparative modeling (CM), fold recognition (FR), and new fold (NF). The FR category was further subdivided into homologues [FR(H)] and analogs [FR(A)] based on evolutionary considerations, and the overlap between assessment categories was classified as CM/FR(H) and FR(A)/NF. CASP5 domains are illustrated in Figure 1. Examples of nontrivial links between CASP5 target domains and existing structures that support our classifications are provided.

Original languageEnglish (US)
Pages (from-to)340-351
Number of pages12
JournalProteins: Structure, Function and Genetics
Volume53
Issue numberSUPPL. 6
DOIs
StatePublished - 2003

Fingerprint

Proteins
Genomics
Theoretical Models
Research

ASJC Scopus subject areas

  • Genetics
  • Structural Biology
  • Biochemistry

Cite this

CASP5 Target Classification. / Kinch, Lisa N.; Qi, Yuan; Hubbard, Tim J P; Grishin, Nick V.

In: Proteins: Structure, Function and Genetics, Vol. 53, No. SUPPL. 6, 2003, p. 340-351.

Research output: Contribution to journalArticle

Kinch, LN, Qi, Y, Hubbard, TJP & Grishin, NV 2003, 'CASP5 Target Classification', Proteins: Structure, Function and Genetics, vol. 53, no. SUPPL. 6, pp. 340-351. https://doi.org/10.1002/prot.10555
Kinch, Lisa N. ; Qi, Yuan ; Hubbard, Tim J P ; Grishin, Nick V. / CASP5 Target Classification. In: Proteins: Structure, Function and Genetics. 2003 ; Vol. 53, No. SUPPL. 6. pp. 340-351.
@article{5c3a17467dcb480a8ba6f940930ca65e,
title = "CASP5 Target Classification",
abstract = "This report summarizes the Critical Assessment of Protein Structure Prediction (CASP5) target proteins, which included 67 experimental models submitted from various structural genomics efforts and independent research groups. Throughout this special issue, CASP5 targets are referred to with the identification numbers T0129-T0195. Several of these targets were excluded from the assessment for various reasons: T0164 and T0166 were cancelled by the organizers; T0131, T0144, T0158, T0163, T0171, T0175, and T0180 were not available in time; T0145 was {"}natively unfolded{"}; the T0139 structure became available before the target expired; and T0194 was solved for a different sequence than the one submitted. Table I outlines the sequence and structural information available for CASP5 proteins in the context of existing folds and evolutionary relationships. This information provided the basis for a domain-based classification of the target structures into three assessment categories: comparative modeling (CM), fold recognition (FR), and new fold (NF). The FR category was further subdivided into homologues [FR(H)] and analogs [FR(A)] based on evolutionary considerations, and the overlap between assessment categories was classified as CM/FR(H) and FR(A)/NF. CASP5 domains are illustrated in Figure 1. Examples of nontrivial links between CASP5 target domains and existing structures that support our classifications are provided.",
author = "Kinch, {Lisa N.} and Yuan Qi and Hubbard, {Tim J P} and Grishin, {Nick V.}",
year = "2003",
doi = "10.1002/prot.10555",
language = "English (US)",
volume = "53",
pages = "340--351",
journal = "Proteins: Structure, Function and Bioinformatics",
issn = "0887-3585",
publisher = "Wiley-Liss Inc.",
number = "SUPPL. 6",

}

TY - JOUR

T1 - CASP5 Target Classification

AU - Kinch, Lisa N.

AU - Qi, Yuan

AU - Hubbard, Tim J P

AU - Grishin, Nick V.

PY - 2003

Y1 - 2003

N2 - This report summarizes the Critical Assessment of Protein Structure Prediction (CASP5) target proteins, which included 67 experimental models submitted from various structural genomics efforts and independent research groups. Throughout this special issue, CASP5 targets are referred to with the identification numbers T0129-T0195. Several of these targets were excluded from the assessment for various reasons: T0164 and T0166 were cancelled by the organizers; T0131, T0144, T0158, T0163, T0171, T0175, and T0180 were not available in time; T0145 was "natively unfolded"; the T0139 structure became available before the target expired; and T0194 was solved for a different sequence than the one submitted. Table I outlines the sequence and structural information available for CASP5 proteins in the context of existing folds and evolutionary relationships. This information provided the basis for a domain-based classification of the target structures into three assessment categories: comparative modeling (CM), fold recognition (FR), and new fold (NF). The FR category was further subdivided into homologues [FR(H)] and analogs [FR(A)] based on evolutionary considerations, and the overlap between assessment categories was classified as CM/FR(H) and FR(A)/NF. CASP5 domains are illustrated in Figure 1. Examples of nontrivial links between CASP5 target domains and existing structures that support our classifications are provided.

AB - This report summarizes the Critical Assessment of Protein Structure Prediction (CASP5) target proteins, which included 67 experimental models submitted from various structural genomics efforts and independent research groups. Throughout this special issue, CASP5 targets are referred to with the identification numbers T0129-T0195. Several of these targets were excluded from the assessment for various reasons: T0164 and T0166 were cancelled by the organizers; T0131, T0144, T0158, T0163, T0171, T0175, and T0180 were not available in time; T0145 was "natively unfolded"; the T0139 structure became available before the target expired; and T0194 was solved for a different sequence than the one submitted. Table I outlines the sequence and structural information available for CASP5 proteins in the context of existing folds and evolutionary relationships. This information provided the basis for a domain-based classification of the target structures into three assessment categories: comparative modeling (CM), fold recognition (FR), and new fold (NF). The FR category was further subdivided into homologues [FR(H)] and analogs [FR(A)] based on evolutionary considerations, and the overlap between assessment categories was classified as CM/FR(H) and FR(A)/NF. CASP5 domains are illustrated in Figure 1. Examples of nontrivial links between CASP5 target domains and existing structures that support our classifications are provided.

UR - http://www.scopus.com/inward/record.url?scp=0242267514&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0242267514&partnerID=8YFLogxK

U2 - 10.1002/prot.10555

DO - 10.1002/prot.10555

M3 - Article

C2 - 14579323

AN - SCOPUS:0242267514

VL - 53

SP - 340

EP - 351

JO - Proteins: Structure, Function and Bioinformatics

JF - Proteins: Structure, Function and Bioinformatics

SN - 0887-3585

IS - SUPPL. 6

ER -