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Updated: Apr 12, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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PR2ALIGN: a stand-alone software program and a web-server for protein sequence alignment using weighted biochemical

Igor B Kuznetsov1, Michael McDuffie2

  • 1Cancer Research Center and Department of Epidemiology and Biostatistics, University at Albany, State University of New York, One Discovery Drive, Rensselaer, NY, 12144, USA. ikuznetsov@albany.edu.

BMC Research Notes
|May 8, 2015
PubMed
Summary

PR2ALIGN offers flexible amino acid sequence alignment using user-defined biochemical properties, outperforming traditional fixed substitution matrices. This novel approach enhances alignment quality by weighting specific biochemical characteristics for greater accuracy.

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