pKa based protonation states and microspecies for protein-ligand docking

ten Brink, Tim; Exner, Thomas E.

pKa based protonation states and microspecies for protein-ligand docking

Files

Exner.pdf(1.53 MB)

Date

2010

Publication type

Journal article

Published in

Journal of Computer-Aided Molecular Design ; 24 (2010), 11. - pp. 935-942. - ISSN 0920-654X. - eISSN 1573-4951

Abstract

In this paper we present our reworked approach to generate ligand protonation states with our structure preparation tool SPORES (Structure PrOtonation and REcognition System). SPORES can be used for the preprocessing of proteins and protein–ligand complexes as e.g. taken from the Protein Data Bank as well as for the setup of 3D ligand databases. It automatically assigns atom and bond types, generates different protonation, tautomeric states as well as different stereoisomers. In the revised version, pKa calculations with the ChemAxon software MARVIN are used either to determine the likeliness of a combinatorial generated protonation state or to determine the titrable atoms used in the combinatorial approach. Additionally, the MARVIN software is used to predict microspecies distributions of ligand molecules. Docking studies were performed with our recently introduced program PLANTS (Protein–Ligand ANT System) on all protomers resulting from the three different selection methods for the well established CCDC/ASTEX clean data set demonstrating the usefulness of especially the latter approach.

Subject (DDC)

540 Chemistry

Keywords

Molecular docking,Input generation,Protomers,ChemAxon MARVIN

Cite This

ISO 690

TEN BRINK, Tim, Thomas E. EXNER, 2010. pKa based protonation states and microspecies for protein-ligand docking. In: Journal of Computer-Aided Molecular Design. 24(11), pp. 935-942. ISSN 0920-654X. eISSN 1573-4951. Available under: doi: 10.1007/s10822-010-9385-x

BibTex

@article{tenBrink2010based-13603,
  year={2010},
  doi={10.1007/s10822-010-9385-x},
  title={pKa based protonation states and microspecies for protein-ligand docking},
  number={11},
  volume={24},
  issn={0920-654X},
  journal={Journal of Computer-Aided Molecular Design},
  pages={935--942},
  author={ten Brink, Tim and Exner, Thomas E.}
}

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