Matthias Wilmanns
EMBL, Postfach 102209, D-69012 Heidelberg, Germany.

David Eisenberg
UCLA, 405 Hilgard, Los Angeles, CA 90024-1570, USA.

Inverted Folding by the Residue Pair Preference Profile Method.

The residue pair profile (R3P) method is an inverted folding method that combines the idea of environmental profiles and pair profile preferences. The method uses statistical preferences for residue pairs. Each pair is created from a profiled residue and a residue in the local environment of the profiled residue. All residue pairs are characterized by their as function of residue types. Each residue pair preference is expressed for all 20 amino acids of the profiled residue and is weighted by the compatability of the environment residue with its own local environment. The R3P method produces an initial profile/sequence alignment which is then refined by converting the initial profile into a profile of a target sequence threaded into the structure of the initial profile.

We have tested this method by evaluating alignments of sequences with known 3D structures using structural superposition as reference. R3P/sequence alignments are >= 50% correct on the average for sequences whose 3D structure pairs superimpose with an rms deviation of <= 1.97A. The average improvement in correctness during this iterative refinement is 14%. The R3P/sequence alignments are compared to sequence/sequence and 3D profile/sequence alignments. When all three methods are combined on the average >= 50% of the alignments are correct for pairs of 3D structures with <= 2.12A.

Single sequences have been screened for compatibility against a R3P database (3044 entries). Examples for built 3D models from sequences of unknown 3D structure, detected with compatible but non-homologous R3Ps, will be presented at the meeting. Possible 3D models for sequences of the structure prediction contest will also be discussed.

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