Graphs Matching

In Part Two, a number of data mining methods were reported that extract relevant bioisosteric pairings from the hterature. The extraction of this information requires graph matching algorithms and fragmentation methods to identify potential bioisosteric substituents. 

Sheridan validated his approach with the MDDR (MDL Drug Data Report) data set of small molecules compiled from the patent literature, retaining only those molecules that contained between 7 and 50 heavy atoms, inclusive. 

1) The MDL Drug Data Report database is available from MDL Information Systems, Inc. at http //www.mdli.com. 

This analysis of 98 445 unique structures over 556 therapeutic areas resulted in a total of 18 275 unique fragment pairs using the preferred algorithms reported. The most frequent fragment parrs identified from this approach were also precedented in the medicinal chemistry literature, suggesting that the method is effective at identifying bioisosteric pairings. 

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BrMK06] G. Brinkmann and B. D. McKay, Fast generation of planar graphs, MATCH 58-2 (2007) 333-367. 

As a complement to question 1, plot the binding data of thiomuscimol in Michaelis-Menten (response versus [L]) format. Try to create a Lineweaver-Burk plot (1/response versus 1/[L]) and perform a linear regression on the data. What is the problem you encounter while making this graph Do your best to graph the data. From the best-fit line of the Lineweaver-Burk plot, determine Kt) and Enva. How well does Ku in this graph match the Ku you determined in... 

Graphs of query and test molecules can be compared by graph matching (subgraph detection) algorithms or systematic comparison of inter-feature distances. Two molecules are considered similar if their pharmacophores match for at least one predicted conformation. In order to explore conformational space and generate conformational ensembles, multiple compound conformations are typically generated by systematic conformational search (in increments) around rotatable bonds. 

Lekishvili, G., On the characterization of molecular stereo structure. 2. The invariants of the two-dimensional graphs, Match, 43, 135-152, 2001. 

Balaban, A.T. (1980). Chemical Graphs. XXXVIII. Synthon Graphs. MATCH (Comm.Math. Comp.Chem.), 8,159-192. 

Bonchev, D., Gutman, I. and Polanski, J. (1987). Parity of the Distance Numbers and Wiener Numbers of Bipartite Graphs. MATCH (Comm.Math.Comp.Chem.), 22,209-214. 

Ivanciuc, O., Balaban, T.-S., Filip, P. and Balaban, A.T. (1992). Design of Topological Indices. Part 7. Analytical Formulae for Local Vertex Invariants of Linear and Monocyclic Molecular Graphs. MATCH (Comm.Math.Comp.Chem.), 28,151-164. 

Skorobogatov, V.A. and Dobrynin, A.A. (1988). Metric Analysis of Graphs. MATCH (Comm. Math.Comp.Chem.), 23,105-151. 

Balaban, A.T, lonescu-Pallas, N. and Balaban, T.-S. (1985) Asymptotic values of topological indices / and / (average distance sum connectivities) for infinite acyclic and cyclic graphs. MATCH Commun. Math. Comput. Chem., 17, 121-146. 

Gutman, L, Graovac, A. and Mohar, B. (1982) On the existence of a Hermitian matrix whose characteristic polynomial is the matching polynomial of a molecular graph. MATCH Commun. Math. Comput. Chem., 13, 129-150. 

On Hosoya polynomials of benzenoid graphs. MATCH Commun. Math. Comput. Chem., 43, 49-66. 

Zhou, B., Gutman, I., De La Pena, J.A., Rada, J. and Mendoza, L. (2007) On spectral moments and energy graphs. MATCH Commun. Math. Comput. Chem., 57, 183-191. 

Melnik S, Garcia-Molina H, Rahm E (2002) Similarity flooding A versatile graph matching algorithm and its application to schema matching. In ICDE. IEEE Computer Society, Washington,... 

For colored graph matching problems, all other atom properties, such as atom types and hybridizations, are also taken into account during the selection of starting atom pairs. 

In the absence of symmetry information, application of a transform to a structure possessing several elements of symmetry produces redundant precursors. The precursors must be created, the redundancies recognized by graph-matching or canonical naming, and finally the duplicate precursors must be deleted. 

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