Daylight Summer School 2001, June 5-7, Santa Fe, NM

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



  1. SMILES Home Page.
  2. Daylight Theory Manual: SMILES-A Simplified Chemical Language
  3. Daylight Theory Manual: SMILES Extensions for Reactions
  4. SMILES, A chemical language and information-system. 1. Introductions to methodology and encoding rules, Weininger D. ABSTRACT
  5. SMILES 2. Algorithm for generation of unique SMILES notation, Weininger D, Weininger A, Weininger JL. ABSTRACT
  6. SMILES 3. Depict: Graphical depiction of chemical structures", Weininger D. ABSTRACT


  1. SMARTS, Daylight Theory Manual
  2. Frequently Asked Questions, SMARTS: Examples
  3. Frequently Asked Questions, "Some SMILES/SMARTS Searching Subtleties"
  4. Dave Weininger, Daylight NewsGroup, A Lesson in Smarts
  5. Recursive SMARTS,Daylight Theory Manual.
  6. 1st-class SMARTS patterns, Sayle R, EuroMUG'97.
  7. "Recursive SMARTS for Synthetic Chemists", Skillman, J., MUG'98.


Substructure, Superstructure and Similarity Searching

  1. Merlin User Guide
  2. Thor User Guide
  3. Introduction to Tversky similarity measure, John Bradshaw, MUG'97.

PCModels, clogp, cmr

  1. Frequently Asked Questions: PCModels FAQ
  2. The History of the Development of CLOGP, Leo A, MUG'98.
  3. "Comparison of programs that calculate octanol-water logP using Starlist", Martin Y, MUG'98.

Clustering Package

  1. Daylight Clustering Manual.
  2. Frequently Asked Questions: Clustering Steps"
  3. Frequently Asked Questions: meargeneighbors vs. nearneighbors-update_file
  4. Use of structure-activity data to compare structure-based clustering methods and descriptors for use in compound selection, Brown RD, Martin YC. ABSTRACT
  5. "Algorithm5: A Procedure for Fuzzy Similarity Clustering", Doman, T, MUG'96.
  6. Techniques for Generating Descriptive Fingerprints in Combinatorial Libraries, Downs GM, Barnard JM. ABSTRACT.
  7. Measuring Diversity: Experimental Design of Combinatorial Libraries for Drug Discovery, Martin EJ, Blaney JM, Siani MA, Spellmeyer DC, Wong AK, Moos WH. ABSTRACT
  8. CLUE: A GUI for cluster browsing", O'Donnell, TJ, MUG'96.
  9. Enhancing the diversity of a corporate database using chemical database clustering and analysis", Shemetulskis NE, Dunbar JB JR, Dunbar BW, Moreland DW, Humblet C. ABSTRACT


  1. Rubicon Reference Manual

Oracle Cartridge

  1. Daylight Chemistry Cartridge,Jack Delany, MUG'00.
  2. Daylight Chemistry Cartridge, Jack Delany, EuroMUG'99.
  3. Dayblob: an ORDBMS-oriented chemical information package, Dave Weininger, MUG'99.

Special Interest Topics

Combinatorial Chemistry

  1. Implementation of a System for Reagent Selection and Library Enumeration, Profiling and Design, Leach, Andrew R., Bradshaw J., Green, Darren V.S., Hann Michael M., Delany, John J. ABSTRACT
  2. A Reaction Based Combinatorial Synthesis Tracking System - Implemented with Java and the Daylight Reaction Toolkit", Liu, M., Tang T., MUG'98.
  3. "Selecting Combinatorial Libraries to Optimise Diversity and Physical Properties", Gillet, V, Willett, P, Bradshaw J, Green D, EuroMUG'97.
  4. "RECAP - Retrosynthetic Combinatorial Analysis Procedure: A Powerful New Technique for Identifying Privileged Molecular Fragments", Lewell, XQ, Duncan J, Watson S, Hann, M, EuroMUG'97.
  5. Use of Markush Structure Techniques to Avoid Enumeration in Diversity Analysis of Large Combinatorial Libraries, Barnard, J, Downs, G, MUG'97.
  6. The Use of Sub-Templates and Super-Templates in Drug Discovery, Geremia, JM, Eyermann CJ, MUG'97.

Daylight Chemical Information Systems Inc.