The repository of tubulin 3d-models as the central milestone of VO CSLabGrid project

  • О. М. Демчук
  • П. А. Карпов
  • С. П. Ожерєдов
  • С. І. Співак
  • М. О. Пидюра
  • Д. О. Самофалова
  • Я. Б. Блюм


Aim. CSModDB database was created as a part of virtual organization (VO) CSLabGrid, to store and manage cytoskeleton proteins three-dimensional models (tubulin, MAPs, FtsZ etc.), as well as to store 3D-models of canonical anti-microtubular agents. The main task of the database is to be a pool of structural models, for virtual molecular screening, molecular docking and rational anti-microtrubule drugs design in the frame of CSLabGrid projects. Methods. The majority of deposed protein models were constructed using I-TASSER server and I-TASSER tool integrated directly in VO environment. Results. 3-D models of tubulin molecules were deposed in *.pdb format. All deposed structures are supplemented by information on the deposition date, modeling method and the author of current model. As a result, stored information is managed with user-friendly graphical interface integrated in VO CSLabGrid infrastructure. Conclusions. Using CSModDB database, established as the part of VO CSLabGrid infrastructure, it was created repository tubulin 3d-models of different taxonomic origin. The models belong to a wide group of parasitic organisms, their potential hosts, as well as a number of model organisms. Such repository not only enables easy data management, but also allows repeated application of tubulin models in new projects of VO CSLabGrid. Now, stored in CSModDB models actively used by VO CSLabGrid participants in fundamental investigations as well as in projects, related to applied projects on design of new anti-microtubule agents.

Keywords: protein structures database, cytoskeleton proteins, tubulins.