title: A swift all-atom energy-based computational protocol to predict DNA-ligand binding affinity and DeltaTm.
abstract: 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.
authors.affiliation: Department of Chemistry, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi 110 016, India.
authors.forename: Saher Afshan
authors.initials: SA
authors.lastname: Shaikh
authors.forename: B
authors.initials: B
authors.lastname: Jayaram
mesh_terms: D055598:Chemical Phenomena; D002627:Chemistry, Physical; D004247:DNA / Q000737:chemistry*; D008024:Ligands; D009690:Nucleic Acid Conformation; D004364:Pharmaceutical Preparations / Q000737:chemistry*; D021281:Quantitative Structure-Activity Relationship; D012997:Solvents; D055672:Static Electricity; D013223:Statistics as Topic; D013696:Temperature; D013816:Thermodynamics
chemical_list: D008024:Ligands; D004364:Pharmaceutical Preparations; D012997:Solvents; D004247:DNA