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A new method in docking for rotatable OH bonds of amino acids in active sites

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We present a new concept in FlexX that determines torsion angles for OH-groups on the receptor side. For the affected amino acids SER, THR, and TYR, hydrogen bonds to neighbouring residues and the ligand are taken into account, providing a more realistic representation of the binding site. This is done irrespective of the ligand type, and without the user's interaction.

We present the concept itself as well as some case studies as early proof-of-concept.

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Correspondence to Angela Rumpl.

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Open Access This article is distributed under the terms of the Creative Commons Attribution 2.0 International License (https://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Rumpl, A., Claußen, H. & Detering, C. A new method in docking for rotatable OH bonds of amino acids in active sites. Chemistry Central Journal 2, P45 (2008) doi:10.1186/1752-153X-2-S1-P45

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Keywords

  • Hydrogen
  • Hydrogen Bond
  • Torsion Angle
  • Realistic Representation
  • Receptor Side