Chemical Structure Representation and Search Systems化学结构表示和搜索系统.ppt

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Chemical Structure Representation and Search Systems化学结构表示和搜索系统.ppt

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ACS National Meeting, Chicago IL, 26 Aug 2001 BCI Ltd., 46 Uppergate Road, Sheffield S6 6BX, UK Chemical Structure Representation and Search SystemsLecture 7. Nov 20, 2003 John Barnard Barnard Chemical Information Ltd Chemical Informatics Software Consultancy Services Sheffield, UK Lecture 7: Topics to be Covered Clustering identifying classes of molecules similar to each other, but different to those in other classes Topological indexes numbers that can be calculated from connection tables Property prediction predicting physicochemical or biological properties directly from connection tables The Drug Discovery Process virtual screening Cluster Analysis process of putting molecules (or other objects) into classes, based on similarity molecules in the same cluster are similar to each other molecules in different clusters are different from each other many different methods and algorithms different clustering methods will result in different clusters, with different relationships between them different algorithms can be used to implement the same method (some may be more efficient than others) Downs, G. M., Barnard, J. M., Rev. Comput. Chem., 18 (2002) Hierarchical and non-hierarchical A basic distinction is between clustering methods that organise clusters hierarchically, and those that do not Hierarchical Agglomerative the hierarchy is built from the bottom upwards several different methods and algorithms basic Lance-Williams algorithm (common to all methods) starts with table of similarities between all pairs of items at each step the most similar pair of molecules (or previously-formed clusters) are merged together until everything is in one big cluster methods differ in how they determine the similarity between clusters “single link” chooses clusters whose closest members are most similar “complete link” chooses clusters whose furthest members are most similar other methods (e.g. Group-average method and Ward’s method) use some sort of “average” memb