References to documentation, papers, presentations, e-mails etc for each topic

Languages

• SMILES
  • SMILES Home Page.
  • Craig James, Dave Weininger, Jack Delany,Daylight Theory Manual, SMILES-A Simplified Chemical Language
  • Jack Delany, "SMILES Extensions for Reactions", Daylight Theory Manual.
  • Citations
    1. WEININGER D, "SMILES, A chemical language and information-system. 1. Introductions to methodology and encoding rules"abstract
    2. WEININGER D, WEININGER A, WEININGER JL,"SMILES 2. Algorithm for generation of unique SMILES notation"abstract
    3. WEININGER D, "SMILES 3. Depict: Graphical depiction of chemical structures",abstract
• SMARTS
  • SMARTS, Daylight Theory Manual
  • Jeremy Yang, Frequently Asked Questions, Writing SMARTS: Some Examples
  • Jeremy Yang, Frequently Asked Questions, "Some SMILES/SMARTS Searching Subtleties"
  • Dave Weininger, Daylight NewsGroup, A Lesson in Smarts
  • Recursive SMARTS,Daylight Theory Manual.
  • Citations
    1. Sayle, R.,1st-class SMARTS patterns,Euro Mug'97.
    2. Skillman, J., "Recursive SMARTS for Synthetic Chemists",Mug '98.

• Substructure, Superstructure and Similarity Searching
  • Jeremy Yang,Merlin User Guide
  • Jeremy Yang,Thor User Guide
  • Citations
    1. Bradshaw J,Introduction to Tversky similarity measure,Mug '97.
• PCModels, clogp, cmr
  • Citations
    1. Leo A,"The History of the Development of CLOGP", Mug '98.
    2. Martin Y,"Comparison of programs that calculate octanol-water logP using Starlist", Mug '98.
• Clustering Package
  • Dave Weininger, Jack Delany, Daylight Clustering Manual.
  • Jeremy Yang, Frequently Asked Questions,"Clustering Steps".
  • Jeremy Yang, Frequently Asked Questions,"meargeneighbors vs. nearneighbors-update_file"
  • Jeremy Yang, 4.51 Top Bugs,"BUG: Nearneighbors semaphore handling errors"
  • Citations
    1. Brown RD, Martin YC,"Use of structure-activity data to compare structure-based clustering methods and descriptors for use in compound selection"abstract
    2. Doman, T. "Algorithm5: A Procedure for Fuzzy Similarity Clustering",Mug '96.
    3. Downs GM, Barnard JM,"Techniques for Generating Descriptive Fingerprints in Combinatorial Libraries",abstract.
    4. Martin EJ, Blaney JM, Siani MA, Spellmeyer DC, Wong AK, Moos WH,"Measuring Diversity: Experimental Design of Combinatorial Libraries for Drug Discovery",abstract
    5. O'Donnell, T.J.,CLUE: A GUI for cluster browsing",Mug '96.
    6. Shemetulskis NE, Dunbar JB JR, Dunbar BW, Moreland DW, Humblet C,"Enhancing the diversity of a corporate database using chemical database clustering and analysis",abstract
• Rubicon
  • Dave Weininger,Rubicon Reference Manual.

• Combinatorial Chemistry
  • Liu, M., Tang T., A Reaction Based Combinatorial Synthesis Tracking System - Implemented with Java and the Daylight Reaction Toolkit", Mug '98.
  • Gillet, V.,Willett, P.,Bradshaw J.,Green D.,"Selecting Combinatorial Libraries to Optimise Diversity and Physical Properties", EuroMug'97.
  • Lewell, X.Q., Duncan J.,Watson S.,Hann, M.,"RECAP - Retrosynthetic Combinatorial Analysis Procedure: A Powerful New Technique for Identifying Privileged Molecular Fragments", EuroMug '97.
  • Barnard, J., Downs, G. "Use of Markush Structure Techniques to Avoid Enumeration in Diversity Analysis of Large Combinatorial Libraries",Mug '97.
  • Geremia, J.M.,Eyermann C.J.,"The Use of Sub-Templates and Super-Templates in Drug Discovery", Mug '97.

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