Artificial Intelligence - Making Use of Reasoning | p. 1 |
Synthesis Planning by Computer | p. 6 |
Other Programs to Support Chemical Synthesis Planning | p. 16 |
Programs that are Similar to LHASA in their Approach | p. 16 |
SECS and PASCOP | p. 16 |
SYNLMA | p. 17 |
SYNCHEM and SYNCHEM2 | p. 18 |
SYNGEN | p. 19 |
SYNSUP-MB and CAOSP | p. 21 |
RESYN | p. 22 |
SOS, MARSEIL, CONAN HOLOWin and GRAAL | p. 23 |
AIPHOS and SOPHIA | p. 24 |
Chiron | p. 24 |
CICLOPS, EROS and WODCA - a Different Approach | p. 25 |
PIRExS | p. 27 |
COSYMA | p. 28 |
CAMEO - Predicting Reactions | p. 28 |
What Happened to Synthesis Planning by Computer? | p. 29 |
International Repercussions of the Harvard LHASA Project | p. 35 |
Structure Representation | p. 41 |
Wiswesser Line-Formula Notation | p. 41 |
SMILES, SMARTS and SMIRKS | p. 43 |
CHMTRN and PATRAN | p. 45 |
ALCHEM | p. 49 |
Molfiles, SDfiles and RDfiles | p. 50 |
Mol2 files | p. 51 |
The Standard Molecular Data Format and Molecular Information File | p. 51 |
Chemical Markup Language | p. 52 |
Using Pictures | p. 52 |
Structure, Sub-Structure and Super-Structure Searching | p. 55 |
Exact Structure Searching | p. 55 |
Canonical SMILES Codes | p. 56 |
Morgan Names and SEMA Names | p. 59 |
MOLGEN-CID | p. 63 |
The Method Described by Henrickson and Toczko | p. 64 |
InChI Code | p. 65 |
Atom by Atom Matching | p. 67 |
Substructure Searching | p. 68 |
Set Reduction | p. 70 |
Superstructure and Markush Structure Searching | p. 74 |
Reaction Searching | p. 75 |
Protons that Come and Go | p. 78 |
Dealing with Tautomerism | p. 78 |
Implicit and Explicit Hydrogen Atoms | p. 81 |
Aromaticity and Stereochemistry | p. 85 |
Aromaticity | p. 85 |
Stereochemistry | p. 88 |
Tetrahedral Centres | p. 89 |
Double Bonds | p. 91 |
Other Kinds of Asymmetry | p. 93 |
Derek - Predicting Toxicity | p. 94 |
How DEREK Came About | p. 94 |
The Alert-based Approach to Toxicity Prediction in DEREK | p. 97 |
Other Alert-Based Toxicity Prediction Systems | p. 103 |
TOX-MATCH and PHARM-MATCH | p. 103 |
Oncologic | p. 105 |
HazardExpert | p. 107 |
BfR/BgVV System | p. 108 |
ToxTree and Toxmatch | p. 108 |
Environmental Toxicity Prediction | p. 108 |
Rule Discovery | p. 110 |
QSAR | p. 110 |
TopKat | p. 111 |
Multicase | p. 112 |
Other Fragment-Based Systems | p. 113 |
REX | p. 114 |
Using Atom-Centred Fragments | p. 115 |
Other Approaches | p. 116 |
The 2D-3D Debate | p. 119 |
Making Use of Reasoning: Derek for Windows | p. 124 |
Moving on from Just Recognising Alerts in Structures | p. 124 |
The Logic of Argumentation | p. 126 |
Choosing Levels of Likelihood for a System Based on LA | p. 132 |
Derek for Windows | p. 134 |
The Derek for Windows Alert Editor | p. 138 |
Predicting Metabolism | p. 142 |
COMPACT, MetaSite and SPORCalc | p. 143 |
XENO, MetabolExpert and META | p. 144 |
Meteor | p. 146 |
Relative Reasoning | p. 155 |
Predicting Biodegradation | p. 165 |
BESS | p. 166 |
CATABOL | p. 167 |
The UMBBD, PPS and Mepps | p. 167 |
META | p. 172 |
The Future for Prediction of Environmental Degradation | p. 174 |
Other Applications and Potential Applications of Knowledge-Based Prediction in Chemistry | p. 176 |
The Maillard Reaction | p. 176 |
Recording Information about Useful Biological Activity | p. 177 |
Proposing Structural Analogues for Drug Design | p. 178 |
Predicting Product Degradation during Storage | p. 178 |
Designing Production Synthesis Routes | p. 179 |
New Approaches to Chemical Synthesis Planning | p. 180 |
Predicting Ecotoxicity | p. 180 |
Using Knowledge-Based Systems for Teaching | p. 182 |
Evaluation and Validation of Knowledge-Based Systems | p. 183 |
Combining Predictions | p. 191 |
Existing Approaches to Combining Toxicity Predictions | p. 191 |
The OECD (Q)SAR Toolbox | p. 194 |
Combining Predictions about Modes of Action that are Largely Independent | p. 194 |
Combining Metabolism Predictions - the NoMiracle Project | p. 196 |
Combining Different Models and Predictions about Different Properties | p. 197 |
A Subjective View of the Future | p. 201 |
Subject Index | p. 204 |
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