Advanced Protein Alignments Based on Sequence, Structure and Hydropathy Profiles; The Paradigm of the Viral Polymerase Enzyme
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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.
KeywordsSimilarity Algorithms Structure Physicochemistry Evolution Genetics
Mathematics Subject Classification28 40 62 68 92
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- 7.Gille, C.: STRAP: Structure based sequences alignment program. http://www.bioinformatics.org/strap/index2.html
- 8.Gille, C.: Molecular Operating Environment (MOE) (2013). http://www.chemcomp.com
- 11.Hooft, R., Sander, C., Scharf, M., Vriend, G.: The pdbfinder database: a summary of pdb, dssp and hssp information with added value. Comput. Appl. Biosci. CABIOS 12(6), 525–529 (1996)Google Scholar
- 14.Krissinel, E.: Enhanced fold recognition using efficient short fragment clustering. J. Mol. Biochem. 1(2), 76–85 (2012)Google Scholar
- 21.Verlet, L.: Computer “Experiments” on classical fluids. I. Thermodynamical properties of Lennard–Jones molecules. Phys. Rev. Online Arch. (Prola) 159(1), 98–103 (1967)Google Scholar
- 23.Vlachakis, D., Tsagkrasoulis, D., Tsiliki, G., Kossida, S.: The future of structural bioinformatics in the post-genomic era. EMBnet.journal 18(1), 3–5 (2012)Google Scholar
- 24.Vlachakis, D., Tsaniras, S.C., Feidakis, C., Kossida, S.: An in silico 3D study of the biglycan core protein, using homology modelling techniques. J. Mol. Biochem. 2(2), 85–93 (2013)Google Scholar
- 25.Vlachakis, D., Tsiliki, G., Tsagkrasoulis, D., Carvalho, C.S., Megalooikonomou, V., Kossida, S.: Speeding up the drug discovery process: structural similarity searches using molecular surfaces. EMBnet.journal 18(1), 6–9 (2012)Google Scholar