title: Fragment-based error estimation in biomolecular modeling.
abstract: Computer simulations are becoming an increasingly more important component of drug discovery. Computational models are now often able to reproduce and sometimes even predict outcomes of experiments. Still, potential energy models such as force fields contain significant amounts of bias and imprecision. We have shown how even small uncertainties in potential energy models can propagate to yield large errors, and have devised some general error-handling protocols for biomolecular modeling with imprecise energy functions. Herein we discuss those protocols within the contexts of protein-ligand binding and protein folding.
authors.affiliation: Quantum Theory Project, The University of Florida, 2328 New Physics Building, P.O. Box 118435, Gainesville, FL 32611-8435, USA.
authors.forename: John C
authors.initials: JC
authors.lastname: Faver
authors.affiliation: Quantum Theory Project, The University of Florida, 2328 New Physics Building, P.O. Box 118435, Gainesville, FL 32611-8435, USA. Electronic address: kmerz1@gmail.com.
authors.forename: Kenneth M
authors.initials: KM
authors.lastname: Merz
mesh_terms: D000818:Animals; D055808:Drug Discovery / Q000379:methods*; D006801:Humans; D008958:Models, Molecular; D004364:Pharmaceutical Preparations / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding / Q000502:physiology
chemical_list: D004364:Pharmaceutical Preparations