Improved Algorithms for Reaction Mapping

Improved Algorithms for Reaction Mapping

John Crabtree, Dinesh Mehta, Thomas McKinnon, Anthony Dean

Colorado School of Mines

Atomic Reaction MappingAtomic Reaction Mapping

• Critical for the automated analysis of:• Enzymatic Reactions

• Biological Pathways

• Chemical Kinetic Mechanisms

• Reaction Classification• Database Consistency Checking

Problem FormulationProblem 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.

Cut Successive LargestCut Successive Largest

• Complexity is O(n2) x (complexity of naming)• Guaranteed to be efficient• Can add chemical rules

Fewest Bonds FirstFewest 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.

Experimental ResultsExperimental Results

• Gas Research Institute GRI-Mech 3.0• 325 Reactions; CSL 94% 2sec; FBF 100%

15sec

• KEGG / Ligand over 5,000 reactions

Applicable Success

FBF 100% 99%

CSL 100% 84%

Akutsu 45% 82%