Beyond Supersecondary Structure: Physics-Based Sequence Alignment

  • S. RackovskyEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1958)


Traditional approaches to sequence alignment are based on evolutionary ideas. As a result, they are prebiased toward results which are in accord with initial expectations. We present here a method of sequence alignment which is based entirely on the physical properties of the amino acids. This approach has no inherent bias, eliminates much of the computational complexity associated with methods currently in use, and has been shown to give good results for structures which were poorly predicted by traditional methods in recent CASP competitions and to identify sequence differences which correlate with structural and dynamic differences not detectable by traditional methods.

Key words

Sequence alignment Amino acid physical properties Physics-based alignment Evolution-free alignment Homology modeling Protein structure prediction 


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Chemistry and Chemical BiologyCornell UniversityIthacaUSA
  2. 2.Department of Pharmacological SciencesIcahn School of Medicine at Mount SinaiNew YorkUSA

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