This chapter contains sections titled: Introduction Integration Efforts, WWW as Information Resource and Limitations Goals Merits of Federation Rather than Unification The Merits of Unification The Merits of Federation Unifying Disparate Data Models is Difficult, Federating them is Easy Language is a Natural Key HTTP is Appropriate Communication Technology HTTP is Specifically Designed for Collaborative Computing HTTP is the Dominant Communication Protocol Today HTML Provides a Universally Accessible GUI MIME “Text/Plain” and “Application/Octet-Stream” are Important Catch-alls Other MIME Types are Useful One Significant HTTP Work-around is Required Implementation Daylight HTTP Toolkit Metaphorics' Cabinet Library Specific Examples of Federated Services Empath – Metabolic Pathway Chart Planet – Protein–ligand Association Network EC Book – Enzyme Commission Codebook WDI – World Drug Index WOMBAT – World of Molecular Bioactivity TCM (Traditional Chinese Medicines), DCM (Dictionary of Chinese Medicine), PARK (Photo ARKive) and zi4 Cabinet “Download” Service Cabinet Usage Example Deployment and Refinement Local Deployment Intranet Deployment Internet Deployment Online Deployment Conclusions

Chapter II.3 SMILES-A Language for Molecules and Reactions David Weininger, David WeiningerSearch for more papers by this author David Weininger, David WeiningerSearch for more papers by this author Book Editor(s):Prof. Dr. Johann Gasteiger, Prof. Dr. Johann Gasteiger Computer-Chemie-Centrum and Institute, of Organic Chemistry, University of Erlangen-Nürnberg, Nägelsbachstraße 25, 91052 Erlangen, GermanySearch for more papers by this author First published: 08 August 2003 https://doi.org/10.1002/9783527618279.ch5Citations: 2 AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Summary This chapter contains sections titled: Introduction Fundamental Concepts Atom Specification Bond Specification Branch Specification Ring Specification Disconnections Reaction Specification Isomerism Beyond the Valence Model Citing Literature Handbook of Chemoinformatics: From Data to Knowledge in 4 Volumes RelatedInformation

Chapter 5.4 Combinatorics of Organic Molecular Structures David Weininger, David WeiningerSearch for more papers by this author David Weininger, David WeiningerSearch for more papers by this author Book Editor(s):Prof. Dr. Johann Gasteiger, Prof. Dr. Johann Gasteiger Computer-Chemie-Centrum and Institute, of Organic Chemistry, University of Erlangen-Nürnberg, Nägelsbachstraße 25, 91052 Erlangen, GermanySearch for more papers by this author First published: 08 August 2003 https://doi.org/10.1002/9783527618279.ch7d AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Summary This chapter contains sections titled: Introduction Conventions Small n-Hexane Derivatives Caveats Conclusions and Implications Handbook of Chemoinformatics: From Data to Knowledge in 4 Volumes RelatedInformation

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Screening mixtures of synthetic oligomers or fixed templates (e.g., rings) with varying substituents is increasingly the focus of drug discovery programs. CHORTLES is designed and implemented to facilitate representation, storage, and searching of oligomeric and template-based mixtures of any size. Building upon the CHUCKLES method of representing oligomers as both monomer-based sequences and all-atom structures, CHORTLES compactly represents a mixture without explicitly enumerating individual molecules. This method lends itself to a hierarchy relating mixtures to submixtures and individual compounds, as one finds when deconvoluting mixtures in drug lead discovery programs. In addition, we describe two methods of searching mixtures at the monomer level. We also present a simple pictorial representation for describing all components in a mixture, which becomes essential as the list of monomer names is expanded beyond common names (e.g., amino acids).

Dual representation of peptide and non-peptide structures in a chemical database as atomic-level molecular graphs and sequence strings permits chemical substructure and similarity searches as well as sequence-based substring and regular expression searches. CHUCKLES interconverts monomer-based sequences with SMILES, which represent atomic-level molecular graphs. Forward-translation maps peptide or other sequences into SMILES. Back-translation extracts monomer sequences from SMILES. This approach permits a generalized representation of monomers allowing user specification of any monomer. CHUCKLES allows mixing of atoms with user-defined monomer names; that is, monomer representation is consistent with SMILES notation. In addition, oligomer branching and cyclization are handled.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

The design of a generalised program for interpreting connection tables is presented, including a language for describing the external encoding of structural information. Such a program is useful for format conversion or as a front-end to chemical application software. This program has been implemented (GEMINI), and is discussed with examples.

ChemInformVolume 21, Issue 49 Other Subjects ChemInform Abstract: SMILES. Part 3. Depict. Graphical Depiction of Chemical Structures. D. WEININGER, D. WEININGER Daylight Chem. Inf. Syst., New Orleans, LA 70130, USASearch for more papers by this author D. WEININGER, D. WEININGER Daylight Chem. Inf. Syst., New Orleans, LA 70130, USASearch for more papers by this author First published: December 4, 1990 https://doi.org/10.1002/chin.199049322AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat No abstract is available for this article. Volume21, Issue49December 4, 1990 RelatedInformation

ALADDIN is a computer program for the design or recognition of compounds that meet geometric, steric, and substructural criteria. ALADDIN searches a database of three-dimensional structures, marks atoms that meet substructural criteria, evaluates geometric criteria, and prepares a number of files that are input for molecular modification and coordinate generation as well as for molecular graphics. Properties calculated from the three-dimensional structure are described by either properties calculated from the molecule itself or from the molecule as compared to a reference molecule and associated surfaces. ALADDIN was used to design analogues to probe a bioactive conformation of a small molecule and a peptide, to test alternative superposition rules for receptor mapping of the D2 dopamine receptor, to recognize unexpected D2 dopamine agonist activity of existing compounds, and to design compounds to fit a binding site on a protein of known structure. We have found that series designed by ALADDIN show much more subtle variation in shape than do those designed by traditional methods and that compounds can be designed to be very close matches to the objective.

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSMILES. 2. Algorithm for generation of unique SMILES notationDavid Weininger, Arthur Weininger, and Joseph L. WeiningerCite this: J. Chem. Inf. Comput. Sci. 1989, 29, 2, 97–101Publication Date (Print):May 1, 1989Publication History Published online1 May 2002Published inissue 1 May 1989https://pubs.acs.org/doi/10.1021/ci00062a008https://doi.org/10.1021/ci00062a008research-articleACS PublicationsRequest reuse permissionsArticle Views4516Altmetric-Citations881LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSMILES, a chemical language and information system. 1. Introduction to methodology and encoding rulesDavid WeiningerCite this: J. Chem. Inf. Comput. Sci. 1988, 28, 1, 31–36Publication Date (Print):February 1, 1988Publication History Published online1 May 2002Published inissue 1 February 1988https://pubs.acs.org/doi/10.1021/ci00057a005https://doi.org/10.1021/ci00057a005research-articleACS PublicationsRequest reuse permissionsArticle Views12790Altmetric-Citations4077LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts

MENTHOR is a database system for the storage and retrieval of three-dimensional coordinate and charge information on molecules as well as of traditional biological and physical properties. Our molecular graphics system retrieves from MENTHOR structural information in individual molecules and receptor map/macromolecular binding site hypotheses. Substructural searches of MENTHOR are used to find starting coordinates for molecular modeling and traditional database searches of MENTHOR identify compounds for which modeling is needed. It also forms the data to be searched with ALLADDIN, our substructure/geometric search program. MENTHOR expedites molecular modeling by organizing previous work and facilitating transmission of information between individuals. Examples from modeling of D-2 receptor agonists are shown.

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDetermination of polychlorinated biphenyls using multiple regression with outlier detection and eliminationLawrence P. Burkhard and David. WeiningerCite this: Anal. Chem. 1987, 59, 8, 1187–1190Publication Date (Print):April 15, 1987Publication History Published online1 May 2002Published inissue 15 April 1987https://pubs.acs.org/doi/10.1021/ac00135a024https://doi.org/10.1021/ac00135a024research-articleACS PublicationsRequest reuse permissionsArticle Views124Altmetric-Citations27LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts