Bioinformatics Vol. 16 no. 9 2000
Pages 776-785
© 2000 Oxford University Press
Original Paper |
MaxSub: an automated measure for the assessment of protein structure prediction quality
1 Department of Chemistry, Ben Gurion
University, Beer-Sheva 84015, Israel
2 Stockholm Bioinformatics Center, 106 91
Stockholm University, Sweden
3 International Institute of Molecular and
Cell Biology, Ks. Trojdena 4, 02-109 Warsaw, Poland
4 Department of Bioinformatics Computer
Science, Ben Gurion University, Beer-Sheva 84015, Israel
Received on February 17, 2000
; revised on May 5, 2000
; accepted on May 5, 2000
Motivation: Evaluating the accuracy of predicted models is critical for assessing structure prediction methods. Because this problem is not trivial, a large number of different assessment measures have been proposed by various authors, and it has already become an active subfield of research (Moult et al. (1999) Critical assessment of methods of protein structure prediction (CASP): round III. Proteins , Suppl32–6). The CASP (Moult et al. (1997) Critical assessment of methods of proteins structure prediction (CASP): round II. Proteins , Suppl3, Dedicated Issue, Moult et al. (1999) Critical assessment of methods of protein structure prediction (CASP): round III. Proteins , Suppl32–6) and CAFASP (Fischer et al. (1999) CAFASP-1: critical assessment of fully automated structure prediction methods. Proteins , Suppl3, 209–217) prediction experiments have demonstrated that it has been difficult to choose one single, ‘best’ method to be used in the evaluation. Consequently, the CASP3 evaluation was carried out using an extensive set of especially developed numerical measures, coupled with human-expert intervention. As part of our efforts towards a higher level of automation in the structure prediction field, here we investigate the suitability of a fully automated, simple, objective, quantitative and reproducible method that can be used in the automatic assessment of models in the upcoming CAFASP2 experiment. Such a method should (a) produce one single number that measures the quality of a predicted model and (b) perform similarly to human-expert evaluations.
Results: MaxSub is a new and independently developed method that
further builds and extends some of the evaluation methods introduced
at CASP3. MaxSub aims at identifying the largest subset of
atoms of a model that superimpose
‘well’ over the experimental structure, and produces a
single normalized score that represents the quality of the model.
Because there exists no evaluation method for assessment measures of
predicted models, it is not easy to evaluate how good our new
measure is. Even though an exact comparison of MaxSub and the CASP3
assessment is not straightforward, here we use a test-bed extracted
from the CASP3 fold-recognition models. A rough qualitative
comparison of the performance of MaxSub vis-a-vis the human-expert
assessment carried out at CASP3 shows that there is a good agreement
for the more accurate models and for the better predicting groups.
As expected, some differences were observed among the medium to poor
models and groups. Overall, the top six predicting groups ranked
using the fully automated MaxSub are also the top six groups ranked
at CASP3. We conclude that MaxSub is a suitable method for the
automatic evaluation of models.
Availability: MaxSub is available at: http://www.cs.bgu.ac.il/~dfischer/MaxSub/MaxSub.html
Contact: {nomsiew,dfischer}@cs.bgu.ac.il; arne{at}biokemi.su.se; leszek{at}iimcb.gov.pl
Supplementary
Information: Full tables are available at:
http://www.cs.bgu.ac.il/
dfischer/MaxSub/MaxSub.html CASP
web site: http://PredictionCenter.llnl.gov/casp3/CAFASP
web site: http://www.cs.bgu.ac.il/~dfischer/CAFASP2
To whom correspondence should be addressed.
CiteULike 
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