Unsupervised guided docking of covalently bound ligands
| Autor: | Xavier Fradera, Jordi Mestres, Jasmit Kaur |
|---|---|
| Rok vydání: | 2005 |
| Předmět: |
Virtual screening
Chemistry Stereochemistry Thrombin Receptors Cytoplasmic and Nuclear Receptors Cell Surface Plasma protein binding Ligands Combinatorial chemistry Computer Science Applications Enzymes Protein structure Protein–ligand docking Searching the conformational space for docking Covalent bond Docking (molecular) DOCK Drug Discovery Computer Simulation Physical and Theoretical Chemistry Software Protein Binding |
| Zdroj: | Journal of computer-aided molecular design. 18(10) |
| ISSN: | 0920-654X |
| Popis: | An approach for docking covalently bound ligands in protein enzymes or receptors was implemented in MacDOCK, a similarity-driven docking program based on DOCK 4.0. This approach was tested with a small number of covalent ligand-protein structures, using both native and non-native protein structures. In all cases, MacDOCK was able to generate orientations consistent with the known covalent binding mode of these complexes, with a performance similar to that of other docking programs. This method was also applied to search for known covalent thrombin inhibitors in a medium-sized molecular database (ca. 11,000 compounds). Detection of functional groups suitable for covalent docking was carried out automatically. A significant enrichment in known active molecules in the first 5% of the database was obtained, showing that MacDOCK can be used efficiently for the virtual screening of covalently bound ligands. |
| Databáze: | OpenAIRE |
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