How to extend the use of grid-based interaction energy maps from chemistry to biotopics.
Many computational tools routinely used in chemistry could successfully be applied to the biosciences since protein-protein and protein-ligand interactions are governed by the laws of chemistry. This paper shows that it is possible to extend the use of existing computational tools from their traditional application field (e.g. chemistry) to culturally-related research areas by the implementation of simple but well-designed utilities. In particular, a computational strategy obtained by combining GRID (the program originally designed by Peter Goodford, and now distributed by Molecular Discovery Ltd.) and BIOCUBE4mf (an application freely available at www.casmedchem.unito.it) was used to a) characterize the surface properties of the cavity of the Bacillus anthracis protective antigen heptameric prepore; b) suggest how to design mutagenesis experiments; c) quantitatively show the selectivity of the KvAP channel for K(+) over Na(+) ions and d) rationalize the pharmacokinetic behavior of 1,4-DHP third-generation drugs.
Caron
Giulia
G
CASMedChem Laboratory, Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Via P. Giuria 9, I-10125 Torino, Italy.
Nurisso
Alessandra
A
Ermondi
Giuseppe
G
D019943:Amino Acid Substitution; D015239:Arylsulfotransferase; D001408:Bacillus anthracis / Q000378:metabolism; D019295:Computational Biology; D016208:Databases, Factual; D004095:Dihydropyridines / Q000493:pharmacokinetics; D008958:Models, Molecular; D016297:Mutagenesis, Site-Directed; D024642:Potassium Channels, Voltage-Gated / Q000737:chemistry; D017434:Protein Structure, Tertiary; D012984:Software; D015238:Sulfotransferases / Q000737:chemistry; D013816:Thermodynamics
D004095:Dihydropyridines; D024642:Potassium Channels, Voltage-Gated; C038806:1,4-dihydropyridine; D015238:Sulfotransferases; D015239:Arylsulfotransferase; C403170:monoamine-sulfating phenol sulfotransferase