Abstract
In this chapter, a scheme of the application of molecular quantum similarity matrices to describe a molecular property of interest is exposed. Quantum similarity matrices need to be conveniently transformed when employed as descriptor source in QSAR procedures. In order to describe the usual transformations, dimensionality reduction and variable selection techniques will be discussed. Combination of different quantum similarity matrices, constituting the Tuned QSAR model, is also discussed. Since the only relevant test for the procedure protocol is its application on real cases, quantum similarity matrices will be used to study three different molecular sets in order to provide the reader with reliable quantitative equations for activity prediction.
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References
Van de Waterbeemd H (1996) Chemometric Methods used in Drug Discovery. In: Van de Waterbeemd H (ed) Structure-Property Correlations in Drug Design. Academic Press, San Diego
Cuadras CM, Fortiana J (2000) The Importance of Geometry in Multivariate Analysis and some Applications. In: Rao CR, Szekely GJ (eds) Statistics for the 21st Century, Marcel Dekker, New York, pp 93–108
Torgerson WS (1952) Multidimensional scaling: I. Theory and method. Psychometrika 17:401–419
Richardson MW (1938) Psychological Bulletin 35:659–660
Eckart C, Young G (1936) The approximation of one matrix by another of lower rank. Psychometrika 1:211–218
Young G, Householder AS (1938) Discussion of a set of points in terms of their mutual distances. Psychometrika 3:19–22
De Leeuw J, Heiser W (1982) Theory of multidimensional scaling. In: Krishnaiah PR, Kanal LN (eds) Handbook of Statistics, Vol 2. North Holland, Amsterdam, pp 285–316
Mardia KV, Kent JT, Bibby JM (1979) Multivariate Analysis. Academic Press, London
Gower JC, Legendre P (1986) Metric and Euclidean properties of dissimilarity coefficients. J Class 3:5–48
Cuadras CM, Arenas C (1990) A distance based regression model for prediction with mixed data. Commun Statist Theor Meth 19:2261–2279
Cuadras CM, Arenas C, Fortiana J (1996) Some computational aspects of a distance-based model for prediction. Commun Statist Simula 25:593–609
Amat L, Robert D, Besalü E, Carbô-Dorca R (1998) Molecular Quantum Similarity Measures Tuned QSAR: An Antitumoral Family Validation Study. J Chem Inf Comput Sei 38:624–631
Demidovich BP, Maron IA (1981) Computational Mathematics. Mir Publishers, Moscow
Pierre DA (1969) Optimization Theory with Applications. John Wiley, New York
Carbó R, Besalü E (1994) Definition, mathematical examples and quantum chemical applications of nested summation symbols and logical Kronecker deltas. Computers Chem 18:117–126
Carbó R, Besalü E (1995) Definition and quantum chemical applications of nested summation symbols and logical functions: Pedagogical artificial intelligence devices for formulae writing, sequential programming and automatic parallel implementation. J Math Chem 18:37–72
Hadjipavlou-Litina D, Hansch C (1994) Quantitative structure-activity relationships of the benzodiazepines. A review and reevaluation. Chem Rev 94:1483–1505
Dewar MJS, Zoebisch EG, Healy EF, Stewart JJP (1985) AMI: A new general purpose quantum chemical molecular model. J Am Chem Soc 107:3902–3909
Kaiser KLE (ed) (1987) QSAR in environmental toxicology. Reidel Publishing Company, Dordrecht
Hutzinger O (ed) (1989) Handbook of environmental chemistry. Springer-Verlag, Berlin
Rekker RF (1977) The hydrophobic fragmental constants. Its derivation and application. A means of the characterization membrane systems. In: Nauta WT, Rekker RF (eds) Pharmacochemistry Library. Elsevier, New York, Vol 1
Amat L, Carbó-Dorca R, Ponec R (1998) Molecular quantum similarity measures as an alternative to log P values in QSAR studies. J Comput Chem 19:1575–1583
Verhaar HJM, Mulder W, Hermens JLM, Rorije E, Langenberg JH, Peijnenburg WJGM, Sabljic A, Güsten H, Eriksson L, Sjöström M, Müller M, Hansen B, Nouwen J, Karcher W (1995) Overview of Structure-Activity Relationships for Environmental Endpoints. Part 1: General Outline and Procedure. Report of the EU-DG-XII Project QSAR for Predicting Fate and Effects of Chemicals in the Environment. (Contract #EV5V-CT92-0211)
Urrestarazu E, Vaes WHJ, Verhaar HJM, Hermens JLM (1998) Quantitative Structure-Activity Relationships for the Aquatic Toxicity of Polar and Nonpolar Narcotic Pollutants. J Chem Inf Comput Sci 38:845–852
AMPAC 6.0,1994 Semichem, 7128 Summit, Shawnee, KS 66216 D.A
Cattell RB (1966) the scree test for the number of factors. Multivariate Behavioral Research 9:331–341
Oxender DL, Fox CF (eds) (1987) Protein Engineering. Alan R. Liss, New York, pp 221–224
Leatherbarrow RJ, Fersht AJ (1986) Protein Engineering. Protein Eng 1:7–16
Hellberg S, Sjostrom M, Skagerberg B, Wold S (1987) Peptide quantitative structure-activity relationships, a multivariate approach. J Med Chem 30:1126–1135
Kato A, Yutani K (1988) Correlation of surface properties with conformational stabilities of wild-type and six mutant tryptophan synthase alpha-subunits substituted at the same position. Protein Eng 2:153–156
Lee C, Levitt M (1991) Accurate prediction of the stability and activity effects of site-directed mutagenesis on a protein core. Nature 352:448–451
Collantes ER, Dunn WJ III (1995) Amino acid side-chain descriptors for quantitative structure-activity relationship studies of peptide analogues. J Med Chem 38:2705–2713
Zbilut JP, Giuliani A, Webber CL Jr, Colosimo A (1998) Recurrence quantification analysis in structure-function relationships of proteins: an overview of a general methodology applied to the case of TEM-1 beta-lactamase. Protein Eng 11:87–93
Hutchison CA III, Phillips S, Edgell MH, Gillam S, Jahnke P, Smith M (1978) Mutagenesis at a specific position in a DNA sequence. J Biol Chem 253:6551–6560
DeSantis G, Berglund P, Stabile MR, Gold M, Jones JB (1998) Site-directed mutagenesis combined with chemical modification as a strategy for altering the specificity of the SI and SV pockets of subtilisin Bacillus lentus. Biochem 37:5968–5973
Mei HC, Liaw YC, Li YC, Wang DC, Takagi H, Tsai YC (1998) Engineering subtilisin YaB: restriction of substrate specificity by the substitution of Gly124 and Gly151 with Ala. Protein Eng 11:109–117
Narinx E, Baise E, Gerday C (1997) Subtilisin from psychophilic antarctic bacteria: characterization and site-directed mutagenesis of residues possibly ivolved in the adaptation to cold. Protein Eng 10:1271–1279
Takagi H, Ohtsu I, Nakamori S (1997) Construction of novel subtilisin E with high specificity, activity and productivity through multiple amino acid substitutions. Protein Eng 10:985–989
Stauffer CE, Etson D (1969) The effect of subtilisin activity on oxidizing a methionine residue. J Biol Chem 244:5333–5338
Estell DA, Graycar TP, Wells JA (1985) Engineering an enzyme by site-directed mutagenesis to be resistant to chemical oxidation. J Biol Chem 260:6518–6521
Wells JA, Vasser M, Powers DB (1985) Cassette mutagenesis: an efficient method for generation of multiple mutations at defined sites. Gene 34:315–323
PC Spartan Plus, Wavefunction Inc., Irvine, CA 92612 USA
Damborsky J (1998) Quantitative structure-function and structure-stability relationships of purposely modified proteins. Protein Eng 11:21–30
Nakai K, Kidera A, Kanehisa M (1988) Cluster analysis of amino acid indices for prediction of protein structure and function. Protein Eng 2:93–100
Tomii K, Kanehisa M (1996) Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng 9:27–36
Kawashima S, Ogata H, Kanehisa M (1999) AAindex: amino acid index database. Nucleic Acids Res 27:368–369
Sneath PH (1966) Relations between chemical structure and biological activity in peptides. J Theor Biol 12:157–195
Oobatake M, Ooi T (1977) An analysis of non-bonded energy of proteins. J Theor Biol 67:567–584
Wells JA, Powers DB, Bott RR (1987) In: Oxender DL, Fox CF (eds) Protein engineering. Alan R Liss, New York, pp 279–287
Robert D, Gironés X, Carbó-Dorca R (1999) Quantification of the influence of single-point mutations on Haloalkane dehalogenase activity: a quantum similarity study. J Chem Inf Comput Sci. in press
Carbo-Dorca R, Amat L, Besalú E, Gironés X, Robert D (1999) Quantum molecular similarity: theory and applications to the evaluation of molecular properties, biological activities and toxicity. In: Carbo-Dorca R, Mezey PG (eds) The Fundamentals of Molecular Similarity. Kluwer, New York, in press
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Carbó-Dorca, R., Robert, D., Amat, L., Gironés, X., Besalú, E. (2000). Full molecular quantum similarity matrices as QSAR descriptors. In: Molecular Quantum Similarity in QSAR and Drug Design. Lecture Notes in Chemistry, vol 73. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-57273-9_4
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DOI: https://doi.org/10.1007/978-3-642-57273-9_4
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