The library of spatial structure models of tubulins from pathogenic worms

  • S. I. Spivak Institute of Food Biotechnology and Genomics NAS of Ukraine, Ukraine 04123, Кyiv, Оsipovskogo str., 2A
  • O. M. Demchuk Institute of Food Biotechnology and Genomics NAS of Ukraine, Ukraine 04123, Кyiv, Оsipovskogo str., 2A
  • P. A. Karpov Institute of Food Biotechnology and Genomics NAS of Ukraine, Ukraine 04123, Кyiv, Оsipovskogo str., 2A
  • S. P. Ozheriedov Institute of Food Biotechnology and Genomics NAS of Ukraine, Ukraine 04123, Кyiv, Оsipovskogo str., 2A
  • Ya. B. Blume Institute of Food Biotechnology and Genomics NAS of Ukraine, Ukraine 04123, Кyiv, Оsipovskogo str., 2A
DOI: https://doi.org/10.7124/FEEO.v20.792

Abstract

Aim. The aim of this work is to create library of pathogenic helminths tubulin 3D-models. Created models will be used as targets for in silico screening of new anthelmintic compounds. Methods. Tubulin sequences were obtained from UniProtKB database. Modeling of spatial structure of the proteins was performed using I-TASSER server. Optimization of three-dimensional models geometry was performed in Gromacs using amber03 force field. Results. Based on Uni-ProtKB database analysis, 302 amino acid sequences of α- (105), β- (170) and γ-tubulins (27) of pathogenic worms were selected. 3D-models of selected proteins were built using base protocol. Conclusions. A built 3D models of pathogenic worms tubulins were deposited in CSModDB (http://csmoddb.ifbg.org.ua/comodore/index.php) database. Created library of 3-D structures are suitable for further usage in VO CSLabGrid virtual screening for new compounds.

Keywords: tubulin, pathogenic worms, database, Grid.

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