Molecular docking studies in factor XIa binding site
| Autor: | Vitukudi Narayanaiyengar Balaji, Shashidhar N. Rao, Govardhan A. Balaji |
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| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Chemistry Stereochemistry Organic Chemistry Protein Data Bank (RCSB PDB) Factor XIa Computational biology 01 natural sciences 0104 chemical sciences Analytical Chemistry Inorganic Chemistry 010404 medicinal & biomolecular chemistry 03 medical and health sciences 030104 developmental biology Docking (molecular) Searching the conformational space for docking Binding site Decoy Spectroscopy |
| Zdroj: | Journal of Molecular Structure. 1108:352-369 |
| ISSN: | 0022-2860 |
| Popis: | Factor XIa inhibitors have been identified to have potential as anticoagulants with robust efficacy and low bleeding risks. In light of their significance and the availability of their 3-D X-ray data in the PDB, we present molecular docking studies carried out with a view to obtain docking protocols that will successfully reproduce the experimentally observed protein-ligand interactions in the case of various X-ray ligands. In this context, we have specifically investigated the efficacy of various cross-docking protocols in reproducing experimental data. Our studies demonstrate that an ensemble of the three apo proteins is capable of accurately docking a majority of the X-ray ligands accurately without invoking any additional conformational flexibility than that present in their experimental structures. Further, we demonstrate that such an ensemble is successfully able to enrich a collection of known active factor XIa inhibitors embedded in a decoy database of drug-like molecules. |
| Databáze: | OpenAIRE |
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