Beware of q2!

C. Hansch, A. Leo, Substituent Constants for Correlation Analysis in Chemistry and Biology, Wiley/Interscience, New York, 1979.

A. Tropsha, S.J. Cho, W. Zheng, New tricks for an old dog: development and application of novel QSAR methods for rational design of combinatorial chemical libraries and database mining, in: A.L. Parrill, M.R. Reddy (Eds.), Rational Drug Design: Novel Methodology and Practical Applications, ACS Symposium Series No. 719, 1999, pp. 198–211.

Zheng, 1998, Rational combinatorial library design. 1. Focus-2D: a new approach to the design of targeted combinatorial chemical libraries, J. Chem. Inform. Comput. Sci., 38, 251, 10.1021/ci970095x

Cho, 1998, Rational combinatorial library design. 2. Rational design of targeted combinatorial peptide libraries using chemical similarity probe and the inverse QSAR approaches, J. Chem. Inform. Comput. Sci., 38, 259, 10.1021/ci9700945

S. Clementi, S. Wold, How to choose the proper statistical method, in: H. van de Waterbeemd (Ed.), Chemometrics Methods in Molecular Design, VCH, Weinheim, 1995, pp. 319–338.

S. Wold, PLS for multivariate linear modeling, in: H. van de Waterbeemd (Ed.), Chemometrics Methods in Molecular Design, VCH, Weinheim, 1995, pp. 195–218.

Hoffman, 1999, Quantitative structure–activity relationship modeling of dopamine D(1) antagonists using comparative molecular field analysis, genetic algorithms-partial least-squares, and k nearest neighbor methods, J. Med. Chem., 42, 3217, 10.1021/jm980415j

Ajay, A unified framework for using neural networks to build QSARs, J. Med. Chem. 36 (1993) 3565–3571.

S. Wold, L. Eriksson, Statistical validation of QSAR results, in: H. van de Waterbeemd (Ed.), Chemometrics Methods in Molecular Design, VCH, Weinheim, 1995, pp. 309–318.

Recanatini, 2000, SAR of 9-amino-1,2,3,4-tetrahydroacridine-based acetylcholinesterase inhibitors: synthesis, enzyme inhibitory activity, QSAR, and structure-based CoMFA of tacrine analogues, J. Med. Chem., 43, 2007, 10.1021/jm990971t

Morón, 2000, Molecular determinants of MAO selectivity in a series of indolylmethylamine derivatives: biological activities, 3D-QSAR/CoMFA analysis, and computational simulation of ligand recognition, J. Med. Chem., 43, 1684, 10.1021/jm991164x

V. Austel, Experimental design in synthesis planning and structure–property correlations, in: H. van de Waterbeemd (Ed.), Chemometrics Methods in Molecular Design, Vol. 49, VCH, Weinheim, 1995, p. 62.

Novellino, 1995, Use of comparative molecular field analysis and cluster analysis in series design, Pharm. Acta Helv., 70, 149, 10.1016/0031-6865(95)00014-Z

Norinder, 1996, Single and domain made variable selection in 3D QSAR applications, J. Chemomet., 10, 95, 10.1002/(SICI)1099-128X(199603)10:2<95::AID-CEM407>3.0.CO;2-M

Kubinyi, 1998, Three-dimensional quantitative similarity–activity relationships (3D QSAR) from SEAL similarity matrices, J. Med. Chem., 41, 2553, 10.1021/jm970732a

Cramer III, 1988, Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins, J. Am. Chem. Soc., 110, 5959, 10.1021/ja00226a005

E.A. Coats, The CoMFA steroids as a benchmark dataset for development of 3D QSAR methods, in: H. Kubinyi, G. Folkers, Y.C. Martin (Eds.), 3D QSAR in drug design, Vol. 3, Kluwer Academic Publishers, ESCOM, Dordrecht, 1998, pp. 199–213.

Zheng, 2000, Novel variable selection quantitative structure–property relationship approach based on the k nearest neighbor principle, J. Chem. Inform. Comput. Sci., 40, 185, 10.1021/ci980033m

Dinan, 1999, An extensive ecdysteroid CoMFA, J. Comput.-Aided Mol., Des.13, 185, 10.1023/A:1008052320014

Bucholz, 1999, Synthesis, evolution, and comparative molecular field analysis of 1-phenyl-3-amino-1,2,3,4-tetrahydronaphtalenes as ligands for histamine H1 receptors, J. Med. Chem., 42, 3041, 10.1021/jm980428x

Molconn-Z, http://www.eslc.vabiotech.com/.

Randić, 1975, On characterization on molecular branching, J. Am. Chem. Soc., 97, 6609, 10.1021/ja00856a001

L.B. Kier, L.H. Hall, Molecular Connectivity in Chemistry and Drug Research, Academic Press, New York, 1976.

L.B. Kier, L.H. Hall, Molecular Connectivity in Structure–Activity Analysis, Wiley, New York, 1986.

Kier, 1985, A shape index from molecular graphs, Quant. Struct. Act. Relat., 4, 109, 10.1002/qsar.19850040303

Kier, 1987, Inclusion of symmetry as a shape attribute in kappa-index analysis, Quant. Struct. Act. Relat., 6, 8, 10.1002/qsar.19870060103

Hall, 1990, Determination of topological equivalence in molecular graphs from the topological state, Quant. Struct. Act. Relat., 9, 115, 10.1002/qsar.19900090207

Hall, 1991, The electrotopological state: an atom index for QSAR, Quant. Struct. Act. Relat., 10, 43, 10.1002/qsar.19910100108

Hall, 1991, The electrotopological state: structure information at the atomic level for molecular graphs, J. Chem. Inform. Comput. Sci., 31, 76, 10.1021/ci00001a012

L.B. Kier, L.H. Hall, Molecular Structure Description: The Electrotopological State, Academic Press, New York, 1999.

Kellogg, 1996, The E-state fields. Applications to 3D QSAR, J. Comput. Aid. Mol. Des., 10, 513, 10.1007/BF00134175

Kier, 1991, A differential molecular connectivity index, Quant. Struct. Act. Relat., 10, 134, 10.1002/qsar.19910100208

Petitjean, 1992, Applications of the radius–diameter diagram to the classification of topological and geometrical shapes of chemical compounds, J. Chem. Inform. Comput. Sci., 32, 331, 10.1021/ci00008a012

Wiener, 1947, Structural determination of paraffin boiling points, J. Am. Chem. Soc., 69, 17, 10.1021/ja01193a005

Platt, 1952, Prediction of isomeric differences in paraffin properties, J. Phys. Chem., 56, 328, 10.1021/j150495a009

C. Shannon, W. Weaver, Mathematical Theory of Communication, University of Illinois, Urbana, IL, 1949.

Bonchev, 1981, Isomer discrimination by topological information approach, J. Comput. Chem., 2, 127, 10.1002/jcc.540020202

A. Golbraikh, D. Bonchev, A. Tropsha, Novel chirality descriptors derived from molecular topology, J. Chem. Inform. Comput. Sci. 41 (2001) 147–158.

Gutman, 1975, Graph theory, J. Chem. Phys., 62, 3399, 10.1063/1.430994

Rücker, 1993, Counts of all walks as atomic and molecular descriptors, J. Chem. Inform. Comput. Sci., 33, 683, 10.1021/ci00015a005

D. Bonchev, Overall connectivity and molecular complexity, in: J. Devillers, A.T. Balaban (Eds.), Topological Indices and Related Descriptors, Gordon and Breach, Reading, UK, 1999, pp. 361–401.

Bonchev, 1997, Novel indices for the topological complexity of molecules, SAR/QSAR Env. Res., 7, 23

L. Sachs, Applied Statistics. A Handbook of Techniques, Springer, Berlin, 1984.

MATLAB, http://www.mathworks.com/products/matlab/.

R.D. Clark, D.G. Sprous, J.M. Leonard, Validating models based on large dataset, in: H.-D. Höltje, W. Sippl (Eds.), Rational Approaches to Drug Design. Proceedings of the 13th European Symposium on Quantitative Structure–Activity Relationships, Prous Sci., 2001, 475–485.

A. Golbraikh, D. Bonchev, Y.-D. Xiao, A. Tropsha, Novel chiral topological descriptors and their applications to QSAR, in: H.-D. Höltje, W. Sippl (Eds.), Rational Approaches to Drug Design. Proceedings of the 13th European Symposium on Quantitative Structure–Activity relationships, Aug. 27–Sept. 1, 2000, Duesseldorf, Germany, Prous Science, 2001, 219–223.