3D thinking: Computational aids for the bioanalyst

Bioanalysis

Volumn 5, Issue 4, 2013, Pages 395-398

  Wright, Pat ^a   Alex, Alexander ^b   Pullen, Frank ^a  

^a UNIVERSITY OF GREENWICH   (United Kingdom)

^b Alexander Alex Consulting   (United Kingdom)

Author keywords

computational; density functional theory; mass spectral fragmentation; metabolite identification; physicochemical properties

Indexed keywords

COMPUTER PROGRAM; INFORMATION PROCESSING; MATHEMATICAL COMPUTING; MECHANICS; MOLECULAR MODEL; PHYSICAL CHEMISTRY; PREDICTION; QUANTITATIVE STRUCTURE ACTIVITY RELATION; QUANTITATIVE STRUCTURE PROPERTY RELATION; REVIEW; STATISTICAL ANALYSIS; THINKING;

DATA INTERPRETATION, STATISTICAL; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; SOFTWARE;

EID: 84874039253     PISSN: 17576180     EISSN: 17576199     Source Type: Journal    
DOI: 10.4155/bio.12.332     Document Type: Review

References (17)

1. Todeschini R, Consonni V. Handbook of Molecular Descriptors. Wiley-VCH, Hoboken, NJ, USA (2000).
2. Waterbeemd H, Gifford E . ADMET in silico modeling: towards prediction paradise? Nat. Rev. Drug Discov. 2, 192-204 (2003). (Pubitemid 37361664)
3. Dearden J, Worth A. In Silico Prediction of Physicochemical Properties. Office for Official Publications of the European Communities, Luxembourg (2007).
4. Tyrkkö E, Pelander A, Ojanperä I. Prediction of liquid chromatographic retention for differentiation of structural isomers. Anal. Chim. Acta 720, 142-148 (2012).
5. Smith PA, Sorich MJ, Low LSC, McKinnon RA, Miners JO. Towards integrated ADME prediction: past, present and future directions for modeling metabolism by UDP-glucuronosyltransferases. J. Mol. Graph. Mod. 22, 507-517 (2004). (Pubitemid 38746576)
6. Cruciani G, Carosati E, De Boeck B, Ethirajulu K, Mackie C. MetaSite: understanding metabolism in human cytochromes from the perspective of the chemist. J. Med. Chem. 48(22), 6970-6979 (2005). (Pubitemid 41533118)
7. Long A, Walker JD. Quantitative structure-activity relationships for predicting metabolism and modeling cytochrome P450 enzyme activities. Environ. Toxicol. Chem. 22(8), 1894-1899 (2003). (Pubitemid 37337313)
8. Heinonen M, Rantanen A, Mielikäinen T et al. FiD: a software for ab initio structural identification of product ions from tandem mass spectrometric data. Rapid Commun. Mass Spectrom. 22(19), 3043-3052 (2008).
9. Hill AW, Mortishire-Smith R-J. Automated assignment of high-resolution collisionally activated dissociation mass spectra using a systematic bond disconnection approach. Rapid Commun. Mass Spectrom. 19, 3111-3118 (2005). (Pubitemid 41540740)
10. Wolf S, Schmidt S, Müller-Hannemann M, Neumann S. In silico fragmentation for computer assisted identification of metabolite mass spectra. BMC Bioinformatics 11(1), 148-160(2010).
11. Burke K. Perspective on density functional theory. J. Chem. Phys. 136(50), 150901 (2012).
12. Alex A. Quantum mechanical calculations. In: Medicinal Chemistry in Comprehensive Medicinal Chemistry II (Volume 4). Jonathan Mason (Ed.). Elsevier, Oxford, UK, 379-418 (2007).
13. Wright P, Alex A, Nyaruwata T, Parsons T, Pullen F. Using density functional theory to rationalise the mass spectral fragmentation of maraviroc and its metabolites. Rapid Commun. Mass Spectrom. 24, 1025-1031 (2010).
14. Chenzhong C, Liao, Marc C, Nicklaus MC. Comparison of nine programs predicting pK(a) values of pharmaceutical substances. J. Chem. Inf. Model 49(12), 2801-2812 (2009).
15. Margabandu R, Subramani K. Comparative study of various quantum mechanical descriptors for prediction of ionization constant (pKa) of substituted anilines. Int. J. ChemTech Res. 2(3), 1507-1513 (2010).
16. Bryantsev VS, Diallo MS, Goddard WA 3rd. pKa calculations of aliphatic amines, diamines, and aminoamides via density functional theory with a Poisson-Boltzmann continuum solvent model. J. Phys. Chem. A. 111(20), 4422-4430 (2007). (Pubitemid 46910793)
17. Szaleniec M, Dudzik A, Pawul M, Kozik B. Quantitative structure enantioselective retention relationship for high-performance liquid chromatography chiral separation of 1-phenylethanol derivatives. J. Chromatogr. A 1216(34), 6224-6235 (2009).