1 / 6

Improved Algorithms for Reaction Mapping

Improved Algorithms for Reaction Mapping. John Crabtree, Dinesh Mehta, Thomas McKinnon, Anthony Dean Colorado School of Mines. Atomic Reaction Mapping. Critical for the automated analysis of: Enzymatic Reactions Biological Pathways Chemical Kinetic Mechanisms Reaction Classification

bebe
Download Presentation

Improved Algorithms for Reaction Mapping

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Improved Algorithms for Reaction Mapping John Crabtree, Dinesh Mehta, Thomas McKinnon, Anthony Dean Colorado School of Mines

  2. Atomic Reaction Mapping • Critical for the automated analysis of: • Enzymatic Reactions • Biological Pathways • Chemical Kinetic Mechanisms • Reaction Classification • Database Consistency Checking

  3. Problem Formulation • R1 + … + Rn <=> P1 + … + Pm • Reaction mapping • Let v = vertex in reactant graph • Let w = vertex in product graph • Mapping: w1 = f(v1), w2 = f(v2) • Cost c(v1, v2) = 0 same bond state between w1, w2 • Cost c(v1, v2) = 1 different state between w1, w2 • Number of bonds formed/broken • Given a valid chemical reaction, obtain a mapping of minimum cost.

  4. Cut Successive Largest • Complexity is O(n2) x (complexity of naming) • Guaranteed to be efficient • Can add chemical rules

  5. Fewest Bonds First • CHCO + CHCO <=> CO + CO + CHCH • 11 bonds • 00000000001 00000000010 etc • Search all bit patterns in order of min cost • Theorem: Given a valid chemical equation, FBF will produce a mathematically optimal mapping.

  6. Experimental Results • Gas Research Institute GRI-Mech 3.0 • 325 Reactions; CSL 94% 2sec; FBF 100% 15sec • KEGG / Ligand over 5,000 reactions

More Related