Mathematics in Computer Science

, Volume 11, Issue 2, pp 197–208 | Cite as

Advanced Protein Alignments Based on Sequence, Structure and Hydropathy Profiles; The Paradigm of the Viral Polymerase Enzyme

  • Dimitrios Vlachakis
  • Alexandros Armaos
  • Sophia Kossida


One of the major drawbacks of modern bioinformatics is the fact that protein similarity and blast searches are still based on primary amino acid sequence rather than structural data. Primary sequence searches are inadequate, as they fail to provide a realistic fingerprint for the query protein. Protein function is much more related to protein structure rather than to its amino acid sequence. After all structure is much more conserved than sequence in nature. In this direction and in an effort to bridge this flaw, a novel platform has been developed, which is capable of performing fast similarity searches using protein primary and secondary structural information. The protein secondary structure profile (PSSP) tool is capable of performing conventional blast searches, based on protein sequences, as well as alignments based on a custom made hydropathy substitution matrix that takes into account the physicochemical profile of the amino acids that compose the query protein. Moreover, PSSP is capable of efficiently exploiting protein secondary structural information from the PDB database when available. If the query protein is not indexed in the RCSB PDB database, it will automatically determine the secondary elements of the given protein by performing an ‘on the fly’ secondary structure prediction. All query proteins are then blasted against the RCSB PDB secondary elements database. Hits are scored, ranked and returned to the user via a well-organized and user friendly graphical interface.


Similarity Algorithms Structure Physicochemistry Evolution Genetics 

Mathematics Subject Classification

28 40 62 68 92 


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Copyright information

© Springer International Publishing 2017

Authors and Affiliations

  • Dimitrios Vlachakis
    • 1
  • Alexandros Armaos
    • 1
  • Sophia Kossida
    • 2
  1. 1.Bioinformatics and Medical Informatics TeamBiomedical Research Foundation of the Academy of AthensAthensGreece
  2. 2.University of Montpellier, IMGT®, The International ImMunoGeneTics Information System®, LIGM, IGH, UPR CNRS 1142Montpellier Cedex 5France

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