Evidence of water molecules--a statistical evaluation of water molecules based on electron density

Journal of Chemical Information and Modeling
Eva NittingerMatthias Rarey

Abstract

Water molecules play important roles in many biological processes, especially when mediating protein-ligand interactions. Dehydration and the hydrophobic effect are of central importance for estimating binding affinities. Due to the specific geometric characteristics of hydrogen bond functions of water molecules, meaning two acceptor and two donor functions in a tetrahedral arrangement, they have to be modeled accurately. Despite many attempts in the past years, accurate prediction of water molecules-structurally as well as energetically-remains a grand challenge. One reason is certainly the lack of experimental data, since energetic contributions of water molecules can only be measured indirectly. However, on the structural side, the electron density clearly shows the positions of stable water molecules. This information has the potential to improve models on water structure and energy in proteins and protein interfaces. On the basis of a high-resolution subset of the Protein Data Bank, we have conducted an extensive statistical analysis of 2.3 million water molecules, discriminating those water molecules that are well resolved and those without much evidence of electron density. In order to perform this classification, we int...Continue Reading

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Citations

Jul 16, 2015·Journal of Chemical Information and Modeling·Alexander S BaydenMichelle L Lamb
Jun 1, 2016·Biochimica Et Biophysica Acta·Lada Biedermannová, Bohdan Schneider
Aug 28, 2016·Journal of Computer-aided Molecular Design·Mathias M von BehrenMatthias Rarey
Feb 17, 2017·Journal of Chemical Information and Modeling·Nils-Ole FriedrichJohannes Kirchmair
May 13, 2017·Journal of Medicinal Chemistry·Eva NittingerMatthias Rarey
Jun 22, 2017·Physical Chemistry Chemical Physics : PCCP·Jiří ČernýLada Biedermannová
May 5, 2017·Nucleic Acids Research·Rainer FährrolfesMatthias Rarey
Feb 14, 2019·Journal of Computer-aided Molecular Design·Eva NittingerVickie Tsui
Mar 21, 2017·Journal of Computer-aided Molecular Design·Mathias M von Behren, Matthias Rarey
Jul 25, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Kwang-Eun ChoiNam Sook Kang
Sep 25, 2020·Journal of Computer-aided Molecular Design·Teresa Danielle BergazinDavid L Mobley
Oct 7, 2020·Acta Crystallographica. Section D, Structural Biology·Axl ErikssonEsko Oksanen
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Sep 18, 2020·Current Opinion in Structural Biology·Balázs Zoltán Zsidó, Csaba Hetényi
Oct 30, 2020·Journal of Chemical Information and Modeling·Piotr Setny
Oct 6, 2017·Journal of Chemical Information and Modeling·Agnes MeyderMatthias Rarey
Jul 26, 2018·Journal of the American Chemical Society·Sonja KunstmannStefanie Barbirz
Jul 24, 2018·Journal of Chemical Information and Modeling·Eva NittingerMatthias Rarey
May 24, 2019·Journal of Chemical Information and Modeling·David SchallerGerhard Wolber
Sep 12, 2017·Journal of Chemical Information and Modeling·Therese InhesterMatthias Rarey
May 10, 2017·The Journal of Physical Chemistry. B·Y Kurzweil-SegevYuri Feldman
Nov 2, 2017·Journal of Chemical Theory and Computation·Gregory A RossJonathan W Essex

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