Molecular Diversity

, Volume 10, Issue 1, pp 39–79 | Cite as

Molecular similarity and diversity in chemoinformatics: From theory to applications

  • Ana G. Maldonado
  • J. P. Doucet
  • Michel Petitjean
  • Bo-Tao Fan


This review is dedicated to a survey on molecular similarity and diversity. Key findings reported in recent investigations are selectively highlighted and summarized. Even if this overview is mainly centered in chemoinformatics, applications in other areas (pharmaceutical and medical chemistry, combinatorial chemistry, chemical databases management, etc.) are also introduced. The approaches used to define and descript the concepts of molecular similarity and diversity in the context of chemoinformatics are discussed in the first part of this review. We introduce, in the second and third parts, the descriptions and analyses of different methods and techniques. Finally, current applications and problems are enumerated and discussed in the last part.


chemoinformatics classification methods clustering methods combinatorial chemistry compound selection descriptors drug design high throughput screening library design molecular diversity molecular similarity partitioning selection methods similar property principle validation methods 



Advanced Algorithm Builder


absorption, distribution, metabolism, excretion and toxicity


Artificial Neural Networks


Burden CAS University of Texas (topological descriptors)


Classification And Regression Tree


Chemical Abstract Service (American Chemical Society)

CLIP program

Candidate Ligand Identification Program


COmprehensive DEscriptors for Structural and Statistical Analysis


Comparative Molecular Field Analysis


Comparative Molecular Similarity Indices Analysis


Central Processor Unit


Cluster Significance Analysis


Common SubStructure


Description, Acquisition, Restitution, Computer-aided design


Density Function


Statistical module to calculate the DISSIMilarity index


Dynamic Mapping of Consensus positions


Desoxirribo Nucleic Acid


Software for the calculation of molecular descriptors


Fragments Reduced to an Environment that is Limited


Fragmental Methods




GEometry; Topology and Atom-Weights AssemblY


Gaussian Maximum Likelihood Classification


Generative Topographic Mapping


Human Immunodeficiency Virus


High Throughput Screening


Hierarchic Tree Substructure Search Systems


Highest Occupied Molecular Orbital – Lowest Unoccupied Molecular Orbital




International Union of Pure and Applied Chemistry


K-Nearest Neighbors


Latent Semantic Structure Indexing


Linear Discriminant Analysis


Substructure search system from CambridgeSoft Corporation


Mapping Property distributions of molecular surfaces


MDL Drug Data Report


Molecular electrostatic Potential


Maximal Common Sub-Structure


Molecular Quantum Similarity


Nearest Mean Classifier


Principal Component Analysis


molecular Property characteristic


Quantum Quantitative Structure-Property Relationship


Quantitative Structure-Activity Relationship


Quantitative Structure-Property Relationship


Quantized Surface Complementarity Diversity


Radial Distribution Function


Root Mean Square


Substructure search software (Beilstein Institute of Organic Chemistry & Softron Ltd)


Soft Independent Modeling of Class Analogy


Simplified Molecular Input Line Entry Specification


Support Vector Machines


Total Pharmacophore Diversity




Wiswesser Line Notation


Weighted Holistic Invariant Molecular


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Copyright information

© Springer Science + Business Media, Inc. 2006

Authors and Affiliations

  • Ana G. Maldonado
    • 1
  • J. P. Doucet
    • 1
  • Michel Petitjean
    • 1
  • Bo-Tao Fan
    • 1
  1. 1.ITODYSUniversité Paris 7 – Denis Diderot, CNRS UMR-7086ParisFrance

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