Omega Redux

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Invertible Nitrogens • Geometry must be pyramidal • No stereochemistry specification • No more than 2 ring bonds • Example 1i8z CUP VI, February 2004
User Defined Templates • -fixfile option in <strong>Omega</strong>2 • Molecule fragment provided as file (.mol2, .sdf…) • Entire molecule is constructed around the used defined fragment • Example 4phv CUP VI, February 2004
Page 1 and 2: Omega Redux Matthew T. Stahl CUP VI
Page 3 and 4: Why not Omicron? • Stochastic pro
Page 5 and 6: Makefraglib Statistics • 2.4M ven
Page 7: Generating Ring Conformers • Exoc
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

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