UNIT 3.10 Mathematically Complete Nucleotide and Protein Sequence Searching Using Ssearch

  1. Alexander J. Ropelewski,
  2. Hugh B. Nicholas Jr.,
  3. David W. Deerfield II

Published Online: 1 FEB 2004

DOI: 10.1002/0471250953.bi0310s04

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Ropelewski, A. J., Nicholas, H. B. and Deerfield, D. W. 2004. Mathematically Complete Nucleotide and Protein Sequence Searching Using Ssearch. Current Protocols in Bioinformatics. 4:3.10:3.10.1–3.10.12.

Author Information

  1. Pittsburgh Supercomputing Center, Pittsburgh, Pennsylvania

Publication History

  1. Published Online: 1 FEB 2004
  2. Published Print: DEC 2003


In this unit a protocol is described for predicting the structure of simple transmembrane a-helical bundles. The protocol is based on a global molecular dynamics search (GMDS) of the configuration space of the helical bundle, yielding several candidate structures. The correct structure among these candidates is selected using information from silent amino acid substitutions, employing the premise that only the correct structure must (by definition) accept all of the silent amino acid substitutions. Thus, the correct structure is found by repeating the GMDS for several close homologs and selecting the structure that persists in all of the trials.