CASP2: Report on ab initio predictions

Research output: Contribution to journalArticle

47 Citations (Scopus)

Abstract

Submissions in the ab initio category included predictions of secondary structure, three-dimensional coordinate sets, modes of oligomerization, and residue and secondary structure segment contact patterns. For secondary structure prediction, four groups showed sustained success according the the criterion Q3 ≤ 68 (Q3 = % of residues correctly assigned to the categories helix, strand, and other). The best program, Rost's PHD, scored over this threshold in 13 of its 16 assessable attempts. For the prediction of full three-dimensional coordinates, no group could claim sustained success in prediction of generally correct structures over a range of targets. However, satisfactory predictions were achieved in one case, pig NK-lysin (target 42), a 78-residue protein with three disulfide bridges. For the prediction of contacts, Olmea, Pazos, and Valencia have developed specialized methods for residue-residue proximity patterns, and Gerloff, Joachimiak, Cohen, and Bennet for segment contacts.

Original languageEnglish (US)
Pages (from-to)151-166
Number of pages16
JournalProteins: Structure, Function and Genetics
Volume29
Issue numberSUPPL. 1
DOIs
StatePublished - Dec 1 1997

Fingerprint

Disulfides
Swine
Proteins
Oligomerization
NK-lysin

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Biochemistry
  • Molecular Biology

Cite this

@article{e71d0eb78874410e84a376b78d06767f,
title = "CASP2: Report on ab initio predictions",
abstract = "Submissions in the ab initio category included predictions of secondary structure, three-dimensional coordinate sets, modes of oligomerization, and residue and secondary structure segment contact patterns. For secondary structure prediction, four groups showed sustained success according the the criterion Q3 ≤ 68 (Q3 = {\%} of residues correctly assigned to the categories helix, strand, and other). The best program, Rost's PHD, scored over this threshold in 13 of its 16 assessable attempts. For the prediction of full three-dimensional coordinates, no group could claim sustained success in prediction of generally correct structures over a range of targets. However, satisfactory predictions were achieved in one case, pig NK-lysin (target 42), a 78-residue protein with three disulfide bridges. For the prediction of contacts, Olmea, Pazos, and Valencia have developed specialized methods for residue-residue proximity patterns, and Gerloff, Joachimiak, Cohen, and Bennet for segment contacts.",
author = "Arthur Lesk",
year = "1997",
month = "12",
day = "1",
doi = "10.1002/(SICI)1097-0134(1997)1+<151::AID-PROT20>3.0.CO;2-M",
language = "English (US)",
volume = "29",
pages = "151--166",
journal = "Proteins: Structure, Function and Genetics",
issn = "0887-3585",
publisher = "Wiley-Liss Inc.",
number = "SUPPL. 1",

}

CASP2 : Report on ab initio predictions. / Lesk, Arthur.

In: Proteins: Structure, Function and Genetics, Vol. 29, No. SUPPL. 1, 01.12.1997, p. 151-166.

Research output: Contribution to journalArticle

TY - JOUR

T1 - CASP2

T2 - Report on ab initio predictions

AU - Lesk, Arthur

PY - 1997/12/1

Y1 - 1997/12/1

N2 - Submissions in the ab initio category included predictions of secondary structure, three-dimensional coordinate sets, modes of oligomerization, and residue and secondary structure segment contact patterns. For secondary structure prediction, four groups showed sustained success according the the criterion Q3 ≤ 68 (Q3 = % of residues correctly assigned to the categories helix, strand, and other). The best program, Rost's PHD, scored over this threshold in 13 of its 16 assessable attempts. For the prediction of full three-dimensional coordinates, no group could claim sustained success in prediction of generally correct structures over a range of targets. However, satisfactory predictions were achieved in one case, pig NK-lysin (target 42), a 78-residue protein with three disulfide bridges. For the prediction of contacts, Olmea, Pazos, and Valencia have developed specialized methods for residue-residue proximity patterns, and Gerloff, Joachimiak, Cohen, and Bennet for segment contacts.

AB - Submissions in the ab initio category included predictions of secondary structure, three-dimensional coordinate sets, modes of oligomerization, and residue and secondary structure segment contact patterns. For secondary structure prediction, four groups showed sustained success according the the criterion Q3 ≤ 68 (Q3 = % of residues correctly assigned to the categories helix, strand, and other). The best program, Rost's PHD, scored over this threshold in 13 of its 16 assessable attempts. For the prediction of full three-dimensional coordinates, no group could claim sustained success in prediction of generally correct structures over a range of targets. However, satisfactory predictions were achieved in one case, pig NK-lysin (target 42), a 78-residue protein with three disulfide bridges. For the prediction of contacts, Olmea, Pazos, and Valencia have developed specialized methods for residue-residue proximity patterns, and Gerloff, Joachimiak, Cohen, and Bennet for segment contacts.

UR - http://www.scopus.com/inward/record.url?scp=0031307080&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0031307080&partnerID=8YFLogxK

U2 - 10.1002/(SICI)1097-0134(1997)1+<151::AID-PROT20>3.0.CO;2-M

DO - 10.1002/(SICI)1097-0134(1997)1+<151::AID-PROT20>3.0.CO;2-M

M3 - Article

C2 - 9485507

AN - SCOPUS:0031307080

VL - 29

SP - 151

EP - 166

JO - Proteins: Structure, Function and Genetics

JF - Proteins: Structure, Function and Genetics

SN - 0887-3585

IS - SUPPL. 1

ER -