NAOMI

Overview

NAOMI was a command-line tool to consistently convert different commonly used molecule file formats (SDF, SMILES, MOL2, PDB). It is based on a robust chemical model developed to correctly describe organic molecules, which is highly relevant in drug discovery. Furthermore, NAOMI checks for the chemical validity of molecules and calculates coordinates for hydrogen atoms.

NAOMI was developed in a joint effort by Sascha Urbaczek, Adrian Kolodzik, J. Robert Fischer, and Tobias Lippert in the research group of Prof. Matthias Rarey at the ZBH - Center for Bioinformatics of the University of Hamburg. We are grateful to our partners Inken Groth at Beiersdorf AG, Stefan Heuser at Georg Simon Ohm University, Tanja Schulz-Gasch at F. Hoffmann-La Roche Ltd, Uta Lessel at Boehringer Ingelheim Pharma GmbH & Co. KG and Holger Claußen at BioSolveIT GmbH.

In June 2016, NAOMI was replaced by our new, highly performant universal converter UNICON.

Software Availability

The NAOMI converter was replaced by UNICON .

References

Urbaczek, S.; Kolodzik, A.; Rarey, M. The Valence State Combination Model: A Generic Framework for Handling Tautomers and Protonation States. J Chem Inf Model 2014, 54 (3), 756-766. DOI: https://doi.org/10.1021/ci400724v
Urbaczek, S.; Kolodzik, A.; Groth, I.; Heuser, S.; Rarey, M. Reading PDB: Perception of Molecules from 3D Atomic Coordinates. J Chem Inf Model 2013, 53 (1), 76-87. DOI: https://doi.org/10.1021/ci300358c
Urbaczek, S.; Kolodzik, A.; Fischer, J. R.; Lippert, T.; Heuser, S.; Groth, I.; Schulz-Gasch, T.; Rarey, M. NAOMI: On the Almost Trivial Task of Reading Molecules from Different File Formats. J Chem Inf Model 2011, 51 (12), 3199-3207. DOI: https://doi.org/10.1021/ci200324e