Chemical structure representations and applications in computational toxicity.

Efficient storage and retrieval of chemical structures is one of the most important prerequisite for solving any computational-based problem in life sciences. Several resources including research publications, text books, and articles are available on chemical structure representation. Chemical substances that have same molecular formula but several structural formulae, conformations, and skeleton framework/scaffold/functional groups of the molecule convey various characteristics of the molecule. Today with the aid of sophisticated mathematical models and informatics tools, it is possible to design a molecule of interest with specified characteristics based on their applications in pharmaceuticals, agrochemicals, biotechnology, nanomaterials, petrochemicals, and polymers. This chapter discusses both traditional and current state of art representation of chemical structures and their applications in chemical information management, bioactivity- and toxicity-based predictive studies.

[1]  A. Peter Johnson,et al.  CLiDE Pro: The Latest Generation of CLiDE, a Tool for Optical Chemical Structure Recognition , 2009, J. Chem. Inf. Model..

[2]  Alan L. Goodson.  Graphical Representation of Chemical Structures in Chemical Abstracts Service Publications , 1980, J. Chem. Inf. Comput. Sci..

[3]  Luciana Quadrelli,et al.  A New Linear Representation of Chemical Structures , 1978, J. Chem. Inf. Comput. Sci..

[4]  Jun Xu,et al.  Selecting Diversified Compounds to Build a Tangible Library for Biological and Biochemical Assays , 2010, Molecules.

[5]  James G. Nourse,et al.  Structure searching in chemical databases by direct lookup methods , 1993, J. Chem. Inf. Comput. Sci..

[6]  J. Gasteiger,et al.  Chemoinformatics: A Textbook , 2003 .

[7]  Carlos M. Bowman,et al.  On-Line Storage and Retrieval of Chemical Information. II. Substructure and Biological Activity Searching , 1979, J. Chem. Inf. Comput. Sci..

[8]  K. Nicolaou,et al.  Solid-phase combinatorial synthesis using MicroKan reactors, Rf tagging, and directed sorting. , 2000, Biotechnology and bioengineering.

[9]  Lois E. Fritts,et al.  Using the Wiswesser line notation (WLN) for online, interactive searching of chemical structures , 1982, Journal of chemical information and computer sciences.

[10]  Muthukumarasamy Karthikeyan,et al.  General Melting Point Prediction Based on a Diverse Compound Data Set and Artificial Neural Networks , 2005, J. Chem. Inf. Model..

[11]  N. Null.  The IUPAC International Chemical Identifier (InChI) , 2009 .

[12]  Peter Willett,et al.  Hyperstructure model for chemical structure handling: generation and atom-by-atom searching of hyperstructures , 1992, J. Chem. Inf. Comput. Sci..

[13]  Stuart M. Kaback.  Chemical Structure Searching in Derwent's World Patents Index , 1980, J. Chem. Inf. Comput. Sci..

[14]  Thomas R. Hagadone,et al.  Capturing Chemical Structure Information in a Relational Database System: The Chemical Software Component Approach , 1995, J. Chem. Inf. Comput. Sci..

[15]  Igor I. Strokov,et al.  A New Modular Architecture for Chemical Structure Elucidation Systems , 1996, J. Chem. Inf. Comput. Sci..

[16]  Jure Zupan,et al.  Algorithms for Chemists , 1989 .

[17]  David Bawden,et al.  Comparison of hierarchical cluster analysis techniques for automatic classification of chemical structures , 1981, J. Chem. Inf. Comput. Sci..

[18]  W. T. Wipke,et al.  Stereochemically unique naming algorithm , 1974 .

[19]  Dragos Horvath,et al.  Pharmacophore-based virtual screening. , 2011, Methods in molecular biology.

[20]  David Weininger,et al.  SMILES, 3. DEPICT. Graphical depiction of chemical structures , 1990, J. Chem. Inf. Comput. Sci..

[21]  Hong-wei Yang,et al.  Aromatic compounds biodegradation under anaerobic conditions and their QSBR models. , 2006, The Science of the total environment.

[22]  Hongma Sun,et al.  Pharmacophore-based virtual screening. , 2008, Current medicinal chemistry.

[23]  J. Hughes,et al.  Physiochemical drug properties associated with in vivo toxicological outcomes. , 2008, Bioorganic & medicinal chemistry letters.

[24]  Gareth Jones,et al.  Pharmacophoric pattern matching in files of three-dimensional chemical structures: Comparison of conformational-searching algorithms for flexible searching , 1994, J. Chem. Inf. Comput. Sci..

[25]  T. Zhu,et al.  Air-water gas exchange of organochlorine pesticides in Taihu Lake, China. , 2008, Environmental science & technology.

[26]  Yoshimasa Takahashi,et al.  Automatic identification of molecular similarity using reduced-graph representation of chemical structure , 1992, J. Chem. Inf. Comput. Sci..

[27]  Nick A. Farmer,et al.  An Interactive Computer Graphics System for Processing Chemical Structure Diagrams , 1977, J. Chem. Inf. Comput. Sci..

[28]  Michael F. Lynch,et al.  Computer storage and retrieval of generic chemical structures in patents, 2. GENSAL, a formal language for the description of generic chemical structures , 1981, J. Chem. Inf. Comput. Sci..

[29]  Andrew R. Leach,et al.  An Introduction to Chemoinformatics , 2003 .

[30]  Peter Ertl,et al.  Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions , 2009, J. Cheminformatics.

[31]  Michael F. Lynch,et al.  Computer storage and retrieval of generic structures in chemical patents. 4. An extended connection table representation for generic structures , 1982, J. Chem. Inf. Comput. Sci..

[32]  Wendy A. Warr,et al.  Representation of chemical structures , 2011 .

[33]  Helge Kränz,et al.  Prediction of Material Properties from Chemical Structures. The Clearing Temperature of Nematic Liquid Crystals Derived from Their Chemical Structures by Artificial Neural Networks , 1996, J. Chem. Inf. Comput. Sci..

[34]  Melvin J. Yu.  Natural Product-Like Virtual Libraries: Recursive Atom-Based Enumeration , 2011, J. Chem. Inf. Model..

[35]  Muthukumarasamy Karthikeyan,et al.  Distributed Chemical Computing Using ChemStar: An Open Source Java Remote Method Invocation Architecture Applied to Large Scale Molecular Data from PubChem , 2008, J. Chem. Inf. Model..

[36]  Rüdiger Walentowski.  Unique, Unambiguous Representation of Chemical Structures by Computerization of a Simple Notation , 1980, J. Chem. Inf. Comput. Sci..

[37]  Henry S. Rzepa,et al.  Chemical Markup, XML, and the World Wide Web. 4. CML Schema , 2003, J. Chem. Inf. Comput. Sci..

[38]  Frank Wania,et al.  Assessment of chemical screening outcomes based on different partitioning property estimation methods. , 2010, Environment international.

[39]  Muthukumarasamy Karthikeyan,et al.  Encoding and Decoding Graphical Chemical Structures as Two-Dimensional (PDF417) Barcodes , 2005, J. Chem. Inf. Model..

[40]  Helmut Beierbeck.  Simple stereochemical structure code for organic chemistry , 1982, J. Chem. Inf. Comput. Sci..

[41]  S. Krishnan,et al.  Hash Functions for Rapid Storage and Retrieval of Chemical Structures , 1978, J. Chem. Inf. Comput. Sci..

[42]  G H Hakim Elahi,et al.  The identification of toxicophores for the prediction of mutagenicity, hepatotoxicity and cardiotoxicity , 2005 .

[43]  John M. Barnard,et al.  Clustering of chemical structures on the basis of two-dimensional similarity measures , 1992, J. Chem. Inf. Comput. Sci..

[44]  Egon L. Willighagen,et al.  The Blue Obelisk—Interoperability in Chemical Informatics , 2006, J. Chem. Inf. Model..

[45]  Sheng-Yong Yang,et al.  Pharmacophore modeling and applications in drug discovery: challenges and recent advances. , 2010, Drug discovery today.

[46]  Tamanna Gandhi,et al.  Exploring QSTR and toxicophore of hERG K+ channel blockers using GFA and HypoGen techniques. , 2008, Journal of molecular graphics & modelling.

[47]  Alexandru T. Balaban,et al.  Correlations between chemical structure and normal boiling points of acyclic ethers, peroxides, acetals, and their sulfur analogs , 1992, J. Chem. Inf. Comput. Sci..

[48]  Fabrizio Costa,et al.  Molecular Graph Augmentation with Rings and Functional Groups , 2010, J. Chem. Inf. Model..

[49]  Igor Strokov.  A Compact code for chemical structure storage and retrieval , 1995, J. Chem. Inf. Comput. Sci..

[50]  Matthias Rarey,et al.  Recore: A Fast and Versatile Method for Scaffold Hopping Based on Small Molecule Crystal Structure Conformations , 2007, J. Chem. Inf. Model..

[51]  Louis Hodes,et al.  An Efficient Design for Chemical Structure Searching. II. The File Oraganization , 1978, J. Chem. Inf. Comput. Sci..

[52]  Jürgen Bajorath,et al.  Advanced fingerprint methods for similarity searching: balancing molecular complexity effects. , 2010, Combinatorial chemistry & high throughput screening.

[53]  S. D. D. V. Rughooputh,et al.  Neural Network Based Chemical Structure Indexing , 2001, J. Chem. Inf. Comput. Sci..

[54]  Muthukumarasamy Karthikeyan,et al.  Harvesting Chemical Information from the Internet Using a Distributed Approach: ChemXtreme , 2006, J. Chem. Inf. Model..

[55]  Peter Willett,et al.  Similarity searching in files of three-dimensional chemical structures: Comparison of fragment-based measures of shape similarity , 1994, J. Chem. Inf. Comput. Sci..

[56]  Peter Willett,et al.  Evaluation of relocation clustering algorithms for the automatic classification of chemical structures , 1984, J. Chem. Inf. Comput. Sci..

[57]  George W. A. Milne,et al.  CONCORD and CAMBRIDGE: comparison of computer generated chemical structures with x-ray crystallographic data , 1993, J. Chem. Inf. Comput. Sci..

[58]  R. Webster Homer,et al.  SYBYL Line Notation (SLN): A Versatile Language for Chemical Structure Representation , 1997, J. Chem. Inf. Comput. Sci..

[59]  Arthur Dalby,et al.  Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited , 1992, J. Chem. Inf. Comput. Sci..