Application of Information - Theoretic Concepts in Chemoinformatics

The use of computational methodologies for chemical database mining and molecular similarity searching or structure-activity relationship analysis has become an integral part of modern chemical and pharmaceutical research. These types of computational studies fall into the chemoinformatics spectrum and usually have large-scale character. Concepts from information theory such as Shannon entropy and Kullback-Leibler divergence have also been adopted for chemoinformatics applications. In this review, we introduce these concepts, describe their adaptations, and discuss exemplary applications of information theory to a variety of relevant problems. These include, among others, chemical feature (or descriptor) selection, database profiling, and compound recall rate predictions.

• Publication year

  2010

• Venue

  Inf.

• Publication date

  2010-10-20

• Fields of study

  Chemistry, Computer Science

• Identifiers
  DOI 10.3390/info1020060
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• Information Theory and Statistics

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  2007cited by this paper
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  2007cited by this paper
• Molecular similarity analysis in virtual screening: foundations, limitations and novel approaches.

  2007cited by this paper
• Basic Overview of Chemoinformatics.

  2007cited by this paper
• SHED: Shannon Entropy Descriptors from Topological Feature Distributions

  2006influential reference
• Elements of Information Theory

  2005cited by this paper
• Induction of decision trees

  2004cited by this paper
• Comparison of Fingerprint-Based Methods for Virtual Screening Using Multiple Bioactive Reference Structures

  2004cited by this paper
• A Comparative Study on Feature Selection Methods for Drug Discovery

  2004cited by this paper
• Similarity Searching of Chemical Databases Using Atom Environment Descriptors (MOLPRINT 2D): Evaluation of Performance

  2004cited by this paper
• Evaluation of Mutual Information and Genetic Programming for Feature Selection in QSAR

  2004cited by this paper
• Differential Shannon Entropy Analysis Identifies Molecular Property Descriptors that Predict Aqueous Solubility of Synthetic Compounds with High Accuracy in Binary QSAR Calculations

  2002cited by this paper
• Integration of virtual and high-throughput screening

  2002cited by this paper
• Handbook of Molecular Descriptors

  2002cited by this paper
• Differential Shannon Entropy as a Sensitive Measure of Differences in Database Variability of Molecular Descriptors

  2001cited by this paper
• Chapter 35 – Chemoinformatics: What is it and How does it Impact Drug Discovery.

  1998cited by this paper
• Chemical Similarity Searching

  1998cited by this paper
• Divergence measures based on the Shannon entropy

  1991cited by this paper
• Concepts and applications of molecular similarity

  1990cited by this paper
• On the complexity of graphs and molecules

  1983cited by this paper
• The first general index of molecular complexity

  1981cited by this paper
• Information theory, distance matrix, and molecular branching

  1977cited by this paper
• Symmetry and information content of chemical structures

  1976cited by this paper
• Entropy and the complexity of graphs: III. Graphs with prescribed information content

  1968cited by this paper
• Entropy and the complexity of graphs: IV. Entropy measures and graphical structure

  1968cited by this paper
• ENTROPY AND THE COMPLEXITY OF GRAPHS: II. THE INFORMATION CONTENT OF DIGRAPHS AND INFINITE GRAPHS

  1968cited by this paper
• Entropy and the complexity of graphs. I. An index of the relative complexity of a graph.

  1968cited by this paper
• Entropy and the complexity of graphs

  1967cited by this paper
• A note on the information content of graphs

  1956cited by this paper
• On the information content of graphs: Compound symbols; Different states for each point

  1956cited by this paper
• Life, information theory, and topology

  1955cited by this paper
• The mathematical theory of communication

  1950cited by this paper
• A mathematical theory of communication

  1948cited by this paper

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• Molecular Similarity Searching Based on Deep Belief Networks with Different Molecular Descriptors

  2020cites this paper
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  2020cites this paper
• Improved Deep Learning Based Method for Molecular Similarity Searching Using Stack of Deep Belief Networks

  2020cites this paper
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• Deep Belief Network for Molecular Feature Selection in Ligand-Based Virtual Screening

  2018cites this paper
• Database fingerprint (DFP): an approach to represent molecular databases

  2017cites this paper
• Quantitative Structure-Epigenetic Activity Relationships

  2017cites this paper
• Descriptors and their selection methods in QSAR analysis: paradigm for drug design.

  2016cites this paper
• A Mini-review on Chemoinformatics Approaches for Drug Discovery

  2015cites this paper
• FRAGMENT REWEIGHTING IN LIGAND-BASED VIRTUAL SCREENING ALI AHMED ALFAKIABDALLA ABDELRAHIM

  2013cites this paper
• Progress in the Visualization and Mining of Chemical and Target Spaces

  2013cites this paper
• An enhancement of Bayesian inference network for ligand-based virtual screening using minifingerprints

  2011cites this paper
• An enhancement of bayesian inference network for ligand-based virtual screening using features selection

  2011cites this paper