Дослідження Типових Конформацій Протеїнтирозинфосфатази 1B За Допомогою Докінгу

Abstract

За допомогою докінгу відомих інгібіторів досліджено типові конформації протеїнтирозинфосфатази 1B.Найкращої конформації не виявлено, хоча для кожного інгібітора існує найбільш відповідна конформація.

Testing of a new docking scoring function on the example of inhibitors of protein tyrosine phosphatase 1B

“…As it follows from Table 2, the new scoring function and the new docking scheme provide a substantial improvement. There is practically no correlation between the predicted and calculated binding constants [11]. Now the correlation is much better.…”

“…There are many inhibitors that bind to the enzyme with the open or closed WPD-loop. Using centroids of all clusters we have already performed molecular docking with a modified version of the AutoDock [11]. Unfortunately, we have not found the cluster providing the best docking results.…”

“…That is why the new scoring function was tested in conditions similar to our previous work [11]. The same set of phosphorus containing inhibitors 2 from the NIH database [17] was docked to the same PDB structures representing five typical conformations ISSN 2308-8303 of PTP1B [11]. It is assumed that the inhibitors with phosphonic groups are competitive inhibitors and bind near the catalytic Cys215.…”