Assessing protein-ligand docking for the binding of organometallic compounds to proteins
Autor: | Elisabeth Ortega-Carrasco, Jean-Didier Maréchal, Agustí Lledós |
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Rok vydání: | 2013 |
Předmět: |
Models
Molecular Coordination sphere Protein Conformation Crystallography X-Ray Ligands Organometallic Compounds Humans Computer Simulation Trypsin Enzyme Inhibitors Databases Protein Group 2 organometallic chemistry Electronic properties Binding Sites Chemistry General Chemistry Kinase inhibition Combinatorial chemistry Molecular Docking Simulation Computational Mathematics Kinetics Drug development Protein–ligand docking Docking (molecular) Drug Design Computer-Aided Design Thermodynamics Protein Kinases Algorithms Software Protein Binding |
Zdroj: | Journal of computational chemistry. 35(3) |
ISSN: | 1096-987X |
Popis: | Organometallic compounds are increasingly used as molecular scaffolds in drug development projects; their structural and electronic properties offering novel opportunities in protein-ligand complementarities. Interestingly, while protein-ligand dockings have long become a spearhead in computer assisted drug design, no benchmarking nor optimization have been done for their use with organometallic compounds. Pursuing our efforts to model metal mediated recognition processes, we herein present a systematic study of the capabilities of the program GOLD to predict the interactions of protein with organometallic compounds. The study focuses on inert systems for which no alteration of the first coordination sphere of the metal occurs upon binding. Several scaffolds are used as test systems with different docking schemes and scoring functions. We conclude that ChemScore is the most robust scoring function with ASP and ChemPLP providing with good results too and GoldScore slightly underperforming. This study shows that current state-of-the-art protein-ligand docking techniques are reliable for the docking of inert organometallic compounds binding to protein. |
Databáze: | OpenAIRE |
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