Assessment of ab initio protein structure prediction

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

The assessment of predictions of protein structures from amino acid sequences is related to the question of analyzing the differences between similar natural protein structures to study protein evolution and conformational change. However, assessments present certain special features: the alignment is fixed, unlike evolving proteins which are subject to insertions and deletions, and the character of the differences between predicted and target structures is different in kind from the differences between related known proteins. This report describes the assessment methods used for CASP-2, the recent organized `blind test' of protein structure prediction. This is set in the context of general methods for extraction of similar substructures. It is emphasized that the problem of finding one common similar substructure is much simpler than that of guaranteeing the identification of all common substructures with similarity better than a specified threshold. Software based on the results presented here will make it possible to extract from two protein structures all substructures that have r.m.s. deviations upon optimal superposition no greater than a prespecified value. Applied to a predicted structure and the experimentally-determined coordinates of the target, this will identify any and all three-dimensionally correct features of the prediction.

Original languageEnglish (US)
Title of host publicationProceedings of the Annual International Conference on Computational Molecular Biology, RECOMB
Editors Anon
PublisherACM
Pages163-171
Number of pages9
Publication statusPublished - 1998
EventProceedings of the 1998 2nd Annual International Conference on Computational Molecular Biology - New York, NY, USA
Duration: Mar 22 1998Mar 25 1998

Other

OtherProceedings of the 1998 2nd Annual International Conference on Computational Molecular Biology
CityNew York, NY, USA
Period3/22/983/25/98

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All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Computer Science(all)

Cite this

Lesk, A. (1998). Assessment of ab initio protein structure prediction. In Anon (Ed.), Proceedings of the Annual International Conference on Computational Molecular Biology, RECOMB (pp. 163-171). ACM.