Omega Redux

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<strong>Omega</strong>2 Builder • Fragment molecule by cleaving σ-bonds – Exocyclic attachments – Carbon-heteroatom bonds – Preserve conjugation • Generate and store fragment conformers using makefraglib (fraglib.sdf) • Generate models by assembling on-disk fragments • Enumerate ring conformers using templates • Enumerate invertible nitrogens CUP VI, February 2004
Makefraglib Statistics • 2.4M vendor compounds • 129 Mb fragment library • 81,392 fragments • 40 CPUs ~24 hrs CUP VI, February 2004
Page 1 and 2: Omega Redux Matthew T. Stahl CUP VI
Page 3: Why not Omicron? • Stochastic pro
Page 7 and 8: Generating Ring Conformers • Exoc
Page 9 and 10: User Defined Templates • -fixfile
Page 11 and 12: Reproducing Bioactive Conformations
Page 13 and 14: Version Comparison Boström Perola
Page 15 and 16: Force Field Selection • mmff •
Page 17 and 18: Force Field Comparison Perola RMS M
Page 19 and 20: Force Field Comparison Perola RMS M
Page 21 and 22: Effect of Optimization Perola ~40 m
Page 23 and 24: Conclusions • Omega2 sucks less

Omega Redux

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