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Keywords:

  • Loop;
  • modeling;
  • comparative;
  • substitution tables;
  • homology

Abstract

CODA, an algorithm for predicting the variable regions in proteins, combines FREAD a knowledge based approach, and PETRA, which constructs the region ab initio. FREAD selects from a database of protein structure fragments with environmentally constrained substitution tables and other rule-based filters. FREAD was parameterized and tested on over 3000 loops. The average root mean square deviation ranged from 0.78 Å for three residue loops to 3.5 Å for eight residue loops on a nonhomologous test set. CODA clusters the predictions from the two independent programs and makes a consensus prediction that must pass a set of rule-based filters. CODA was parameterized and tested on two unrelated separate sets of structures that were nonhomologous to one another and those found in the FREAD database. The average root mean square deviation in the test set ranged from 0.76Å for three residue loops to 3.09 Å for eight residue loops. CODA shows a general improvement in loop prediction over PETRA and FREAD individually. The improvement is far more marked for lengths six and upward, probably as the predictive power of PETRA becomes more important.

CODA was further tested on several model structures to determine its applicability to the modeling situation. A web server of CODA is available at http://www-cryst.bioc.cam.ac.uk/∼charlotte/Coda/search_coda.html.