aquaPELE: A Monte Carlo-Based Algorithm to Sample the Effects of Buried Water Molecules in Proteins.

Journal of Chemical Theory and Computation
Martí MunicoyVictor Guallar

Abstract

Water is frequently found inside proteins, carrying out important roles in catalytic reactions or molecular recognition tasks. Therefore, computational models that aim to study protein-ligand interactions usually have to include water effects through explicit or implicit approaches to obtain reliable results. While full explicit models might be too computationally daunting for some applications, implicit models are normally faster but omit some of the most important contributions of water. This is the case of our in-house software, called protein energy landscape exploration (PELE), which uses implicit models to speed up conformational explorations as much as possible; the lack of explicit water sampling, however, limits its model. In this work, we confront this problem with the development of aquaPELE. It is a new algorithm that extends the exploration capabilities while keeping efficiency as it employs a mixed implicit/explicit approach to also take into account the effects of buried water molecules. With an additional Monte Carlo (MC) routine, a set of explicit water molecules is perturbed inside protein cavities and their effects are dynamically adjusted to the current state of the system. As a result, this implementation c...Continue Reading

References

Aug 23, 1996·Journal of Molecular Biology·H LiuW F van Gunsteren
Dec 1, 1995·Journal of Computer-aided Molecular Design·C S Poornima, P M Dean
Dec 1, 1995·Journal of Computer-aided Molecular Design·C S Poornima, P M Dean
May 2, 2002·Journal of Computational Chemistry·Richard H Henchman, J Andrew McCammon
Sep 30, 2005·Journal of Medicinal Chemistry·Marcel L VerdonkRobin Taylor
Oct 8, 2005·Journal of Computational Chemistry·Jay L BanksRonald M Levy
Feb 3, 2007·Journal of Chemical Information and Modeling·Yipin LuShaomeng Wang
Feb 20, 2007·Journal of Chemical Information and Modeling·Christopher R CorbeilNicolas Moitessier
Feb 13, 2008·Journal of the American Chemical Society·Robert AbelRichard A Friesner
Apr 17, 2008·The Journal of Chemical Physics·Giuseppe BrancatoVincenzo Barone
Nov 21, 2008·The Journal of Biological Chemistry·Victor GuallarSyun-Ru Yeh
May 30, 2009·Journal of Computational Chemistry·Zhongqiao Hu, Jianwen Jiang
Jul 2, 2009·Protein Science : a Publication of the Protein Society·Thijs BeumingWoody Sherman
Sep 17, 2009·The Journal of Physical Chemistry. B·Julien MichelWilliam L Jorgensen
Nov 26, 2009·Current Topics in Medicinal Chemistry·Stephanie B A de BeerChris Oostenbrink
May 27, 2011·Bioorganic & Medicinal Chemistry Letters·Pei-Pei KungRobert Kania
Jul 1, 2011·Journal of Chemical Information and Modeling·Gianluca RossatoMartin Smiesko
Oct 28, 2011·Nature·Philip Ball
Dec 21, 2011·Methods in Molecular Biology·Zheng Li, Themis Lazaridis
Mar 6, 2012·Biophysical Journal·M Fátima Lucas, Víctor Guallar
Mar 7, 2012·Bioorganic & Medicinal Chemistry Letters·Jared N CummingAndrew W Stamford
Jan 22, 2013·ACS Medicinal Chemistry Letters·Vassilios MyrianthopoulosAlexios-Leandros Skaltsounis
Apr 13, 2013·Journal of Computer-aided Molecular Design·G Madhavi SastryWoody Sherman
Jul 11, 2013·PloS One·Gordon Lemmon, Jens Meiler
Apr 23, 2014·Journal of Computational Chemistry·Bingjie Hu, Markus A Lill
Jan 8, 2015·Biophysical Journal·Martin KotevVíctor Guallar
Jun 19, 2015·Journal of Medicinal Chemistry·Christopher R SmithCorey Wyrick
Jul 23, 2015·Bioinformatics·Elias D LópezAdrian G Turjanski
Oct 29, 2015·Journal of the American Chemical Society·Gregory A RossJonathan W Essex

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Citations

Jun 10, 2021·The Journal of Physical Chemistry. B·Sergi RodaVictor Guallar
Aug 31, 2021·Current Opinion in Structural Biology·Eleni Michael, Thomas Simonson

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