Adding hydrogen atoms to molecular models via fragment superimposition.

ABSTRACT:

Background

Most experimentally determined structures of biomolecules lack annotated hydrogen positions due to their low electron density. However, thorough structure analysis and simulations require knowledge about the positions of hydrogen atoms. Existing methods for their prediction are either limited to a certain range of molecules or only work effectively on small compounds.

Results

We present a novel algorithm that compiles fragments of molecules with known hydrogen atom positions into a library. Using this library the method is able to predict hydrogen positions for molecules with similar moieties. We show that the method is able to accurately assign hydrogen atoms to most organic compounds including biomacromolecules, if a sufficiently large library is used.

Conclu

SUBMITTER: Kunzmann P 

PROVIDER: S-EPMC8966362 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature