Is the reductionist paradox an Achilles Heel of drug discovery?

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Application of the Shape Group Method to Conformational Processes: Shape and Conjugation Changes in the Conformers of 2-Phenyl-Pyrimidine. Walker, P.D., Mezey, P.G., Maggiora, G.M., Johnson, M.A., and Petke, J.D. J. Comput. Chem. 99, 4947–4954 (1995).

Shape Group Analysis of Molecular Similarity: Shape Similarity of Six-Membered Aromatic Ring Systems. Walker, P.D., Maggiora, G.M., Johnson, M.A., Petke, J.D., and Mezey, P.G. J. Chem. Inf. Comput. Sci. 35, 568–578 (1995).

Solvation Thermodynamics of Polar Molecules in Aqueous Solution by the XRISM Method. Lee, P. H. and Maggiora, G. M. J. Phys. Chem. 97, 10175–10185 (1993).

Looking for Buried Treasures: The Search for New Drug Leads in Large Chemical Data Bases. Maggiora, G. M., Johnson, M. A., Lajiness, M. S., Miller, A. B. and Hagadone, T. R. Mathl. Comput. Modeling 11, 626–629 (1988).

A Characterization of Molecular Similarity Methods for Property Prediction. Johnson, M. A., Basak, S. and Maggiora, G. M. Mathl. Comput. Modeling , 11, 630–634 (1988).

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The Reductionist Paradox: Are the Laws of Chemistry and Physics Sufficient for the Discovery of New Drugs? Maggiora, G.M., J. Comput.-Aided Mol. Design 25, 699–708.

Emergence of the Concept of Molecular Diversity at Pharmacia. Lajiness, M.S., Johnson, M.A., and Maggiora, G.M. Invited submission for a Special Article on “Diverse Viewpoints on Computational Aspects of Molecular Diversity, Y. Martin (Ed.), J. Combinat. Chem. 3, 231–250 (2000).

FORWARD to the book Molecular Structure Description: The Electrotopological State, L.B. Kier & L.H. Hall, Academic Press, San Diego, pp. xiii-xv, forward by Maggiora, G.M. (1999).

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Three Dimensional Chemical Structure Handling. Maggiora, G. M. Book review: by P. Willett, John Wiley & Sons, New York. Comput. Chem. 16, 270 (1992).

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Ab Initio Configuration Interaction and Random Phase Approximation Calculations of the Excited Singlet and Triplet States of Uracil and Cytosine. Petke, J. D., Maggiora, G. M., and Christofferson, R. E. J. Phys. Chem. 96, 6992–7001 (1992).

Ab Initio Configuration Interaction and Random Phase Approximation Calculations of the Excited Singlet and Triplet States of Adenine and Guanine. Petke, J. D., Maggiora, G. M. and Christoffersen, R. E. J. Am. Chem. Soc. 112, 5452–5460 (1990).

Quantum Mechanical SCF/CI Studies as Probes of Macromolecular Structure: Methodological Aspects of Spectral Comparisons. Petke, J. D., Maggiora, G. M. and Christoffersen, R. E. In Computer-Assisted Modeling of Receptor-Ligand Interactions: Theoretical Aspects and Applications to Drug Design , R. Rein, Ed., Alan R. Liss, Inc., New York, pp. 373–383 (1989).

Investigation of Ab Initio HF-SCF-CI Methods for Calculating Rotatory Strengths in (R)-3 Methylcyclobutene. Chabalowsky, C., Maggiora, G.M., and Christoffersen, R.E. J. Am. Chem. Soc . 107, 1632–1640 (1984).

Quantum Mechanical Characterization of the Low-Lying Singlet and Triplet States of Anthraquinone, Quinizarin, and 1,4-Dihydroxy Anthraquinone. Petke, J.D., Butler, P., and Maggiora, G.M. Int. J. Quantum Chem. 27, 71–87 (1984).

Ab Initio Calculations on Large Molecules Using Molecular Fraagments. SCF MO CI Studies of Low-Lying Singlet and Triplet States of Pyrazine. Petke, J.D., Christoffersen, R.E., Maggiora, G.M., and Shipman, L.L. Int. J. Quantum Chem.: Quantum Biol. Symp. No. 4 , pp. 343-355 (1976).

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An Information-Theoretic Characterization of Partitioned Property Spaces. Maggiora, G.M. and Shanmugasundaram, V. J. Math. Chem. 38, 1–2 (2004).

Dipole Sums and Intermolecular Interaction Coefficients Derived from Refractive Index Data. Yoffe, J. A., Maggiora, G. M., and Amos, A. T. Theoret. Chim. Acta 69, 461–473 (1986).

Intermolecular Interaction Energies from Minimal-Basis SCF Calculations. Interactions Pertinent to Formaldehyde Hydration. Maggiora, G.M. and Williams, I.H. J. Mol. Struct. (THEOCHEM), 88, 23–35 (1982).

Development of a Flexible Intra- and Intermolecular Empirical Potential Function for Large Molecular Systems. Oie, T., Maggiora, G.M., Christoffersen, R.E., and Duchamp, D.J. Int. J. Quantum Chem.: Quantum Biol. Symp. No. 8 , pp. 1-49 (1981).

Development of Theoretical Methodology for Large Molecules. Maggiora, G.M., Christoffersen, R.E., Yoffe, J.A., and Petke, J.D. Ann. New York Acad. Sci. 367, 1–16 (1981).

Some Rules for S(-2k) Dipole Sums. Yoffe, J.A., Maggiora, G.M., and Amos, A.T. Theoret. Chim. Acta 58, 137–144 (1981).

The London Approximation and the Calculation of Dispersion Interaction as a Sum of Atom-Atom Terms. Yoffe, J.A. and Maggiora, G.M. Theoret. Chim. Acta 56,191–198 (1980).

Ab Initio Calculations on Large Molecules Using Molecular Fragments. Generalization and Characteristics of Floating Spherical Gaussian Basis Sets. Maggiora, G.M. and Christoffersen, R.E. J. Am. Chem. Soc ., 98, 8325–8332 (1976).

Ab Initio Calculations on Large Molecules Using Molecular Fragments. Unrestricted Hartree-Fock Calculations of the Low-Lying States of Formaldehyde and its Radical Ions. Davis, T.D., Maggiora, G.M., and Christoffersen, R.E. J. Am. Chem. Soc ., 96, 7878–7887 (1974).

Ab Initio Calculations on Large Molecules Using Molecular Fragments. Evaluation and Extension of Initial Procedures. Christoffersen, R.E., Spangler, D., Hall, G.G., and Maggiora, G.M. J. Am. Chem. Soc . 95, 8526–8536 (1973).

Ab Initio Calculations on Large Molecules Using Molecular Fragments. Initial Studies on Open-Shell Systems. Davis, T.D., Christoffersen, R.E., and Maggiora, G.M. Chem. Phys. Letts . 21, 576–580 (1973).

Transferability of Molecular Fragments to Large Molecules. Christoffersen, R.E., Shipman, L.L., and Maggiora, G.M. Int. J. Quantum Chem. 58, 143–149 (1971).

Ab Initio Calculations on Large Molecules Using Molecular Fragments. First-Order Electronic Properties for Hydrocarbons. Maggiora, G.M., Genson, D.E., Christoffersen, R.E., and Cheney, B.V. Theoret. Chim. Acta 22, 337–352 (1971).

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Mixture-based Synthetic Combinatorial Libraries: Direct in vivo Testing, Scaffold Ranking, and Enhanced Deconvolution Using Computational Approaches. Houghten, R. A., Pinilla, C., Appel, J. R., Giulianotti, M. A., Nefzi, A., Ostresh, J. M., Dooley, C.T., Maggiora, G. M., Medina Franco, J. L., Brunner, D., and Schneider, J. J. Comb. Chem. 10, 3–19 (2008).

Synthesis of Platinum(II) Chiral Tetraamine Coordination Complexes. Nefzi, A., Hoesl, C.E., Kauffman, G.B., Maggiora, G.M., and Houghton, R.A. J. Combin. Chem. 8, 780–783 (2006).

An Assessment of the Consistency of Medicinal Chemists in Reviewing Compound Lists. Lajiness, M.S., Maggiora, G.M., and Shanmugasundaram, V. J. Med. Chem. 47, 4891–4896 (2004).

An Introduction to Molecular Similarity and Chemical Spaces. Maggiora, G.M. In Food Science Informatics , K. Martinez-Mayorga & J.L. Medina-Franco, Eds. John Wiley & Sons, New York, pp. 1–81 (2014).

Molecular Similarity Analysis. Medina-Franco, J.L. and Maggiora, G.M. In Chemoinformatics for Drug Discovery, J. Bajorath, Ed., John Wiley & Sons, New York, pp. 343–399 (2014).

Molecular Similarity in Medicinal Chemistry (Mini-Perspective). Maggiora, G.M., Vogt, M., Stumpfe, D., and Bajorath, J. J. Med. Chem. 57, 3186–3204 (2014).

Molecular Similarity Measures. Maggiora, G.M. and Shanmugasundaram, V. In Chemoinformatics and Computational Chemical Biology , 2nd Ed., J. Bajorath, Ed., Humana Press, Springer Science + Business Press, New York, pp. 39–100 (2011).

Molecular Basis Sets - A General Similarity-Based Approach for Representing Chemical Spaces. Raghavendra, A.S. and Maggiora, G.M. J. Chem. Inf. Model. 47, 1328–1340 (2007).

Evaluating Molecular Similarity Using Reduced Representations of the Electron Density. Meurice, N., Maggiora, G.M., and Vercauteren, D.P. J. Mol. Model. 11, 237–247 (2005)

Putting Molecular Similarity into Context: Asymmetric Indices for Field-Based Similarity Measures. Mestres, J. and Maggiora, G.M. J. Math. Chem. 39, 107–118 (2005).

A General Analysis of Field-Based Molecular Similarity Indices. Maggiora, G.M., Petke, J.D., and Mestres, J. J. Math. Chem. 31, 251–270 (2002).

Molecular Similarity Measures. Maggiora, G.M. and Shanmugasundaram, V. In Chemoinformatics: Concepts, Methods, and Tools for Drug Discovery , 1st Ed., J. Bajorath, Ed., Humana Press, Totowa, NJ, pp. 1–50 (2004).

A General Analysis of Field-Based Molecular Similarity Indices. Maggiora, G.M., Petke, J.D., and Mestres, J. J. Math. Chem. 31, 251–270 (2002).

A General Analysis of Field-Based Molecular Similarity Indices. Mestres, J., Rohrer, D.C., and Maggiora, G.M. MIMIC: A Molecular Field Matching Program. Exploiting the Applicability of Molecular Similarity Approaches. J. Comput. Chem. 18, 934–954 (1997).

Four Association Coefficients for Relating Molecular Similarity Measures. Cheng, C., Maggiora, G. M., Lajiness, M.S., and Johnson, M.A. J. Chem. Inf. Comput. Sci. 36, 909–915 (1996).

Molecular Similarity Analysis: Applications in Drug Discovery. Johnson, M. A., Maggiora, G. M., Lajiness, M.S., Moon, J.B., Petke, J.D., and Rohrer, D.C. Chemometric Methods in Molecular Design , H.V. Waterbeemd, Ed., Verlag-Chemie, Weinheim, pp. 89–110 (1994).

Introduction to Similarity in Chemistry. Maggiora, G. M. and Johnson, M. A. In Concepts and Applications of Molecular Similarity , M.A. Johnson and G.M. Maggiora, Eds., John Wiley & Sons, New York, Chapter 1 (1990).

Concepts and Applications of Molecular Similarity (Book). Johnson, M. A. and Maggiora, G. M., Eds. John Wiley & Sons, New York, pp. 393 (1990).

Molecular Similarity: A Basis for Designing Drug Screening Programs. Johnson, M. A., Lajiness, M. S. and Maggiora, G. M. In QSAR: Quantitative Structure-Activity Relationships in Drug Design, J.L. Fauchère, Ed., Alan Liss, Inc., New York, pp. 173–176 (1989).

Implementing Drug Screening Programs Using Molecular Similarity Methods. Lajiness, M. S., Johnson, M. A. and Maggiora, G. M. In QSAR: Quantitative Structure-Activity Relationships in Drug Design , J.L. Fauchère, Ed., Alan Liss, Inc., New York, pp. 167–171 (1989).

Comparison of bioactive chemical space networks generated using substructure- and fingerprint-based measures of molecular similarity. Zhang, B., Vogt, M., Maggiora, G.M., and Bajorath, J. J. Comput.-Aided Mol. Design 29, 595–608 (2015).

Design and characterization of chemical space networks for different compound data sets. Zwierzyna, M., Vogt, M., Maggiora, G.M., and Bajorath, J. J. Comput.-Aided Mol. Design 29, 113–125 (2015).

Chemical space networks – a powerful new paradigm for the description of chemical spaces. Maggiora, G.M. and Bajorath, J. J. Comput.-Aided Mol. Design 28, 795–802 (2014).

Artificial Neural Networks: A New Computational Paradigm with Applications in Chemistry. Maggiora, G. M. and Elrod, D. W. Proceedings, 16th International On-Line Information Meeting , 8–10 December 1992, London, England, pp. 109–125 (1992).

Computational Neural Networks as Model-Free Mapping Devices. Maggiora, G. M., Elrod, D. W., and Trenary, R. G., J. Chem. Inf. Comp. Sci ., 32, 732–741 (1992).

Predicting Chemical Reactions with a Neural Network. Elrod, D. W., Maggiora, G. M., and Trenary, R. G., Predicting Chemical Reactions with a Neural Network. Computing in the 90's. The First Great Lakes Computer Science Conference Proceedings ," N. A. Sherwani, E. de Doncker, and J. A. Kapenga, Eds., Springer-Verlag, Berlin, pp. 392–398 (1991).

Applications of Neural Networks in Chemistry. 2. A General Connectivity Representation for the Prediction of Regiochemistry. Elrod, D. W., Maggiora, G. M., and Trenary, R. G. Tetrahedron Comput. Meth. 3, 163–174 (1990).

Applications of Neural Networks in Chemistry. 1. Prediction of Electrophilic Aromatic Substitution Reactions. Elrod, D. W., Maggiora, G. M. and Trenary, R. G. J. Chem. Inf. Comput. Sci . 30, 477–484 (1990).

Reaction-Surface Topography for Hydride Transfer: ab initio MO Studies of Isoelectronic Systems CH3O + CH2O and CH3NH2 + CH2NH2. Williams, I. H., Miller, A. B., and Maggiora, G. M. J. Am. Chem. Soc . 112, 530–537 (1990).

Linearity and the Unimportance of Tunneling in Hydride Transfer: Ab Initio MO Studies. Hutley, B. G., Mountain, A. E., Williams, I. H., Maggiora, G. M., and Schowen, R. L. Chem. Comm. 267–268 (1986).

Theoretical Probes of Activated-Complex Structure and Properties: Substituent Effects in Carbonyl Addition. Williams, I. H., Spangler, D., Maggiora, G. M., and Schowen, R. L. J. Am. Chem. Soc. 107, 7717–7723 (1985).

Determination and Characterization of a Transition-State for Water Formaldehyde Addition. Spangler, D., Williams, I.H., and Maggiora, G.M. J. Comput. Chem. 4, 524–541(1983).

Theoretical Models for Solvation and Catalysis in Carbonyl Addition. Williams, I.H., Spangler, D., Femec, D.A., Maggiora, G.M., and Schowen, R.L. J. Am. Chem. Soc . 105 31–40 (1983).

The Structure of Dinitrogen Pentoxide. Carpenter, J. and Maggiora, G.M. Chem. Phys. Letts . 87, 349–352 (1982).

Use and Abuse of the Distinguished-Coordinate Method in Transition-State Structure Searches. Williams, I.H. and Maggiora, G.M. J. Mol. Struct. (THEOCHEM) 89, 365–378 (1982).

Theoretical Models for Mechanism and Catalysis in Carbonyl Addition. Williams, I.H., Maggiora, G.M., and Schowen, R.L. J. Am. Chem. Soc. 102, 7831–7839 (1980).

Theoretical Models of Transition-State Structure and Catalysis in Carbonyl Addition. Williams, I.H., Spangler, D., Femec, D.A., Maggiora, G.M., and Schowen, R.L. J. Am. Chem. Soc. 102, 6619–6621(1980).

Quantum Mechanical Approaches to the Study of Enzymic Transition States. Maggiora, G.M. and Christoffersen, R.E. In Transition States in Biochemical Processes , R.L. Schowen and R.D. Gandour (Eds.), Plenum Press, New York, pp. 119–163 (1978).

The Interplay of Theory and Experiment in Bio-Organic Chemistry: Three Case Histories. Maggiora, G.M. and Schowen, R.L. In A Survey of Bio-Organic Chemistry, E.E. Van Tamelin (Ed.), Academic Press, New York, pp. 173–229 (1977).

Excited States of All-trans and 11-cis Retinal. All Valence-Electron SCF MO CI Calculations. Weimann, L.J., Maggiora, G.M., and Blatz, P.E. Int. J. Quantum Chem.: Quantum Biol. Symp. No. 2 , pp. 9-24 (1975).

Proton Bridges in Enzyme Catalysis. Elrod, J.P., Gandour, R.D., Hogg, J.L., Kise, M., Maggiora, G.M., Schowen, R.L., and Venkatasuban, K.S. In Faraday Symposia of the Chemical Society , No. 10, pp. 145–153 (1975).

Ab Initio Calculations on Large Molecules Using Molecular Fragments. Nitroxide Spin-Label Characterizations. Davis, T.D., Maggiora, G.M., and Christoffersen, R.E. J. Am. Chem. Soc . 97, 1347–1356 (1974).

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