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
    • WEININGER D, "SMILES, A chemical language and information-system. 1. Introductions to methodology and encoding rules"abstract
    • WEININGER D, WEININGER A, WEININGER JL,"SMILES 2. Algorithm for generation of unique SMILES notation"abstract
    • 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
    • Sayle, R.,1st-class SMARTS patterns,Euro Mug'97.
    • Skillman, J., "Recursive SMARTS for Synthetic Chemists",Mug '98.

Packages

• Substructure, Superstructure and Similarity Searching
  • Jeremy Yang,Merlin User Guide
  • Jeremy Yang,Thor User Guide
  • Citations
    • Bradshaw J,Introduction to Tversky similarity measure,Mug '97.
• PCModels, clogp, cmr
  • Jeremy Yang, Frequently Asked Questions, "PCModels FAQ"
  • Citations
    • Leo A,"The History of the Development of CLOGP", Mug '98.
    • 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
    • Brown RD, Martin YC,"Use of structure-activity data to compare structure-based clustering methods and descriptors for use in compound selection"abstract
    • Doman, T. "Algorithm5: A Procedure for Fuzzy Similarity Clustering",Mug '96.
    • Downs GM, Barnard JM,"Techniques for Generating Descriptive Fingerprints in Combinatorial Libraries",abstract.
    • Martin EJ, Blaney JM, Siani MA, Spellmeyer DC, Wong AK, Moos WH,"Measuring Diversity: Experimental Design of Combinatorial Libraries for Drug Discovery",abstract
    • O'Donnell, T.J.,CLUE: A GUI for cluster browsing",Mug '96.
    • 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.