Molecular Dynamics as a pattern recognition tool: an automated process detects peptides that preserve the 3D arrangement of Trypsin's Active Site (Journal article)

Tatsis, V. A./ Stavrakoudis, A./ Demetropoulos, I. N.

Recently, the synthesis of a molecule has been reported that belongs to a Lysine based, branched cyclic peptide class. This work explores the ability of such molecules to preserve the 3D geometry of the Trypsin's Active Site (TAS) by applying an integrated framework of automated computer procedures. The following four factors a) D/L chirality, b) different amino acids at different positions of the molecular scaffold's cyclic part, c) the application of AMBER and CHARMM force fields and d) different implicit solvation models were evaluated against TAS similarity. It was found that a number of molecules exhibit satisfactory geometric affinity to the TAS during extended Molecular Dynamics runs. We estimated that more than 2000 molecules (belonging to this class) could retain good similarity to the TAS arrangement.
Institution and School/Department of submitter: Πανεπιστήμιο Ιωαννίνων. Σχολή Οικονομικών και Κοινωνικών Επιστημών. Τμήμα Οικονομικών Επιστημών
Keywords: *Automation,Binding Sites,Peptides/*chemistry,Stereoisomerism,Trypsin/*chemistry
URI: https://olympias.lib.uoi.gr/jspui/handle/123456789/11158
ISSN: 0301-4622
Link: http://www.ncbi.nlm.nih.gov/pubmed/18177993
Appears in Collections:Άρθρα σε επιστημονικά περιοδικά ( Ανοικτά)

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