A swift all-atom energy-based computational protocol to predict DNA-ligand binding affinity and DeltaTm
| Autor: | Saher Afshan Shaikh, Bhyravabhotla Jayaram |
|---|---|
| Rok vydání: | 2007 |
| Předmět: |
Quantitative structure–activity relationship
Chemical Phenomena Stereochemistry Binding energy Static Electricity Statistics as Topic Drug design Quantitative Structure-Activity Relationship Ligands chemistry.chemical_compound Computational chemistry Drug Discovery Static electricity Atom Protocol (object-oriented programming) Chemistry Chemistry Physical Temperature DNA Pharmaceutical Preparations Yield (chemistry) Solvents Molecular Medicine Nucleic Acid Conformation Thermodynamics |
| Zdroj: | Journal of medicinal chemistry. 50(9) |
| ISSN: | 0022-2623 |
| Popis: | A hybrid molecular mechanics-statistical mechanics-solvent accessibility-based computational protocol is developed to calculate DNA-ligand binding affinity without any database training and is validated on 50 DNA-ligand complexes. The calculated binding energies yield high correlation coefficients of 0.95 (R2 = 0.90) and 0.96 (R2 = 0.93) in linear plots against experimental binding free energies (DeltaGo) and DeltaTm, respectively. The protocol is translated into a swift, web-enabled, freely accessible computational tool, http://www.scfbio-iitd.res.in/preddicta, for DeltaGo and DeltaTm prediction for DNA-ligand complexes to aid and expedite rational drug design attempts. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
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