QSAR studies using the parashift systemFootnote†

^†This paper is dedicated to the memory of our colleague and dear friend Martyn Ford who passed away in June 2007.

References

• Glen , RC and Rose , VS . 1987 . Computer program suite for the calculation, storage and manipulation of molecular property and activity descriptors . J. Mol. Graph. , 5 : 79 – 86 .
   Google Scholar
• Hyde , RM and Livingstone , DJ . 1988 . Perspectives in QSAR: computer chemistry and pattern recognition . J. Comp.-Aid. Mol. Design , 2 : 145 – 157 .
   PubMed Web of Science ®Google Scholar
• Verloop , A , Hoogenstraaten , W and Tipker , J . 1976 . “ Development and application of new steric substituent parameters in drug design ” . In Drug Design , Edited by: Ariens , EJ . Vol. VII , 165 – 207 . New York : Academic Press .
   Google Scholar
• Katritzky , AR , Slavov , SH , Dobchev , DA and Karelson , M . 2007 . Comparison between 2D and 3D-QSAR approaches to correlate inhibitor activity for a series of indole amide hydroxamic acids . QSAR Comb. Sci. , 26 : 333 – 345 .
   Google Scholar
• Kubinyi , H , ed. 1993 . 3D QSAR in Drug Design: Theory Methods and Applications , Leiden : ESCOM .
   Google Scholar
• Goodford , PJ . 1996 . Multivariate characterization of molecules for QSAR analyses . J. Chemom. , 10 : 107 – 111 .
   Web of Science ®Google Scholar
• Klebe , G , Abraham , U and Metzner , T . 1994 . Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity . J. Med. Chem. , 37 : 4130 – 4146 .
   PubMed Web of Science ®Google Scholar
• Silverman , BD and Platt , DE . 1996 . Comparative molecular moment analysis (CoMMA): 3D-QSAR without molecular superposition . J. Med. Chem. , 39 : 2129 – 2140 .
   PubMed Web of Science ®Google Scholar
• Bursi , R , Dao , T , van Wijk , T , de Gooyer , M , Kellenbach , E and Verwer , P . 1999 . Comparative spectra analysis (CoSA): spectra as three-dimensional molecular descriptors for the prediction of biological activities . J. Chem. Inf. Comput. Sci. , 39 : 861 – 867 .
   PubMedGoogle Scholar
• Doweyko , AM . 1988 . The hypothetical active site lattice. An approach to modelling active sites from data on inhibitor molecules . J. Med. Chem. , 31 : 1396 – 1406 .
   PubMed Web of Science ®Google Scholar
• Livingstone , DJ . 1991 . Pattern recognition methods for use in rational drug design, in Molecular Design and Modeling: Concepts and Applications , Edited by: Langone , JJ . 613 – 638 . New York : Academic Press . Vol. 203 of Methods in Enzymology
   Google Scholar
• Livingstone , DJ . 1995 . Data Analysis for Chemists: application to QSAR and Chemical Product Design , Oxford : Oxford University Press .
   Google Scholar
• Livingstone , DJ . 2000 . The Characterisation of chemical structures using molecular properties–a survey . J. Chem. Inf. Comput. Sci. , 40 : 195 – 209 .
   PubMedGoogle Scholar
• Clark , T . 2003 . “ Modelling the Chemistry: time to break the mould? ” . In EuroQSAR 2002: designing Drugs and Crop Protectants , Edited by: Ford , M , Livingstone , DJ , Dearden , J and van de Waterbeemd , H . 111 – 121 . Oxford : Blackwell Publishing .
   Google Scholar
• Ehresmann , B , Martin , B , Horn , AHC and Clark , T . 2003 . Local molecular properties and their use in predicting reactivity . J. Mol. Model. , 9 : 342 – 347 .
   Google Scholar
• Ehresmann , B , de Groot , MJ , Alex , A and Clark , T . 2004 . New molecular descriptors based on local properties at the molecular surface and a boiling-point model derived from them . J. Chem. Inf. Comput. Sci. , 44 : 658 – 668 .
   Google Scholar
• Ehresmann , B , de Groot , MJ and Clark , T . 2005 . Surface-integral QSPR models: local energy properties . J. Chem. Inf. Model. , 45 : 1053 – 1060 .
   Google Scholar
• Foster , R , Hyde , RM and Livingstone , DJ . 1978 . A substituent constant for drug design based on the properties of organic electron-donor-acceptor complexes . J. Pharm. Sci. , 67 : 1310 – 1312 .
   Google Scholar
• Livingstone , DJ , Hyde , RM and Foster , R . 1979 . Further study of an organic electron-donor-acceptor related substituent constant . Eur. J. Med. Chem. , 14 : 393 – 397 .
   Google Scholar
• Livingstone , DJ , Greenwood , R , Rees , R and Smith , MD . 2002 . Modelling mutagenicity using properties calculated by computational chemistry . SAR QSAR Environ. Res. , 13 : 21 – 33 .
   PubMed Web of Science ®Google Scholar
• Livingstone , DJ , Evans , DA and Saunders , MR . 1992 . Investigation of a charge-transfer substituent constant using computer chemistry and pattern recognition techniques . J. Chem. Soc. Perkin , II : 1545 – 1550 .
   Google Scholar
• 2000 . Tsar 3.3 , Oxford : Oxford Molecular Ltd .
   Google Scholar
• Turner , DB , Willlett , P , Ferguson , AM and Heritage , TW . 1999 . Evaluation of a novel molecular vibration-based descriptor (EVA) for QSAR studies: 2. Model validation using a benchmark steroid dataset . J. Comput-aid. Mol. Design , 13 : 271 – 296 .
   Google Scholar
• Todeschini , R and Gramatica , P . 1997 . 3D-modelling and prediction by WHIM descriptors. Part 5. Theory development and chemical meaning of the WHIM descriptors . Quant. Struct.-Act. Relat. , 16 : 113 – 119 .
   Google Scholar
• Horn , AHC , Lin , Jr-H and Clark , T . 2005 . Multipole electrostatic model for MNDO-like techniques with minimal valence spd-basis sets . Theoretica Chimica Acta , 114 : 159 – 168 .
   Google Scholar
• Clark , T , Lin , Jr-H and Horn , AHC . 2004 . ParaSurf 1.0 , Erlangen : Computer-Chemie-Centrum, University of Erlangen .
   Google Scholar
• Ritchie , DW . 2007 . ParaFit’07 , Kempston, , UK : University of Aberdeen and Cepos InSilico Ltd . see www.ceposinsilico.com
   Google Scholar
• Contact Cepos InSilico for details of these algorithms (www.ceposinsilico.de)
   Google Scholar
• Clark , T , Lin , Jr-H and Horn , AHC . 2007 . ParaSurf’07 , Kempston, , UK : Universitaet Erlangen-Nuernberg and Cepos InSIlico Ltd . www.ceposinsilico.com
   Google Scholar