Strategy to discover diverse optimal molecules in the small molecule universe.

Journal Article (Journal Article)

The small molecule universe (SMU) is defined as a set of over 10(60) synthetically feasible organic molecules with molecular weight less than ∼500 Da. Exhaustive enumerations and evaluation of all SMU molecules for the purpose of discovering favorable structures is impossible. We take a stochastic approach and extend the ACSESS framework ( Virshup et al. J. Am. Chem. Soc. 2013 , 135 , 7296 - 7303 ) to develop diversity oriented molecular libraries that can generate a set of compounds that is representative of the small molecule universe and that also biases the library toward favorable physical property values. We show that the approach is efficient compared to exhaustive enumeration and to existing evolutionary algorithms for generating such libraries by testing in the NKp fitness landscape model and in the fully enumerated GDB-9 chemical universe containing 3 × 10(5) molecules.

Full Text

Duke Authors

Cited Authors

  • Rupakheti, C; Virshup, A; Yang, W; Beratan, DN

Published Date

  • March 2015

Published In

Volume / Issue

  • 55 / 3

Start / End Page

  • 529 - 537

PubMed ID

  • 25594586

Pubmed Central ID

  • PMC4372820

Electronic International Standard Serial Number (EISSN)

  • 1549-960X

International Standard Serial Number (ISSN)

  • 1549-9596

Digital Object Identifier (DOI)

  • 10.1021/ci500749q


  • eng