Improved Algorithms for Reaction Mapping

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%