Assessment of ab initio protein structure prediction

Research output: Contribution to conferencePaperpeer-review


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)
Number of pages9
StatePublished - 1998
EventProceedings of the 1998 2nd Annual International Conference on Computational Molecular Biology - New York, NY, USA
Duration: Mar 22 1998Mar 25 1998


OtherProceedings of the 1998 2nd Annual International Conference on Computational Molecular Biology
CityNew York, NY, USA

All Science Journal Classification (ASJC) codes

  • General Computer Science
  • General Biochemistry, Genetics and Molecular Biology


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