Molecular Quantum Similarity in QSAR and Drug Design

1 Introduction.- 1.1 Origins and evolution of QSAR.- 1.2 Molecular similarity in QSAR.- 1.3 Scope and contents of the book.- 2 Quantum objects, density functions and quantum similarity measures.- 2.1 Tagged sets and molecular description.- 2.2 Density functions.- 2.3 Quantum objects.- 2.4 Expectation values in Quantum Mechanics.- 2.5 Molecular Quantum Similarity.- 2.6 General definition of molecular quantum similarity measures (MQSM).- 2.7 Quantum self-similarity measures.- 2.8 MQSM as discrete matrix representations of the quantum objects..- 2.9 Molecular quantum similarity indices (MQSI).- 2.10 The Atomic Shell Approximation (ASA).- 2.11 The molecular alignment problem.- 3 Application of Quantum Similarity to QSAR.- 3.1 Theoretical connection between QS and QSAR.- 3.2 Construction of the predictive model.- 3.3 Possible alternatives to the multilinear regression.- 3.4 Parameters to assess the goodness-of-fit.- 3.5 Robustness of the model.- 3.6 Study of chance correlations.- 3.7 Comparison between the QSAR models based on MQSM and other 2D and 3D QSAR methods.- 3.8 Limitations of the models based on MQSM.- 4 Full molecular quantum similarity matrices as QSAR descriptors.- 4.1 Pretreatment for quantum similarity matrices.- 4.2 The MQSM-QSAR protocol.- 4.3 Combination of quantum similarity matrices: the tuned QSAR model.- 4.4 Examples of QSAR analyses from quantum similarity matrices.- 5 Quantum self-similarity measures as QSAR descriptors.- 5.1 Simple QSPR models based on QS-SM.- 5.2 Characterization of classical 2D QSAR descriptors using QS-SM.- 5.3 Description of biological activities using fragment QS-SM.- 6 Electron-electron repulsion energy as a QSAR descriptor.- 6.1 Connection between the electron-electron repulsion energy and QS-SM.- 6.2 ?Vee? as a descriptorfor simple linear QSAR models.- 6.3 Evaluation of molecular properties using ?Vee? as a descriptor.- 7 Quantum similarity extensions to non-molecular systems: Nuclear Quantum Similarity.- 7.1 Generality of Quantum Similarity for quantum systems.- 7.2 Nuclear Quantum Similarity.- 7.3 Structure-property relationships in nuclei.- 7.4 Limitations of the approach.- References.