Zobrazeno 1 - 10
of 102
pro vyhledávání: '"Berk Hess"'
Publikováno v:
Scientific Reports, Vol 8, Iss 1, Pp 1-13 (2018)
Abstract Aquaporin TIP2;1 is a protein channel permeable to both water and ammonia. The structural origin of ammonia selectivity remains obscure, but experiments have revealed that a double mutation renders it impermeable to ammonia without affecting
Externí odkaz:
https://doaj.org/article/53c03b2ba91844bead5b1dffce09ba6b
Autor:
Arne Elofsson, Berk Hess, Erik Lindahl, Alexey Onufriev, David van der Spoel, Anders Wallqvist
Publikováno v:
PLoS Computational Biology, Vol 15, Iss 1, p e1006649 (2019)
Externí odkaz:
https://doaj.org/article/2c6e294ddf4f46458505a7136b4b5411
Autor:
Mark James Abraham, Teemu Murtola, Roland Schulz, Szilárd Páll, Jeremy C. Smith, Berk Hess, Erik Lindahl
Publikováno v:
SoftwareX, Vol 1, Iss , Pp 19-25 (2015)
GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of calculation types, preparation and analysis tools. Several advanced technique
Externí odkaz:
https://doaj.org/article/55cadcc886944e3dacd5bf642323b442
Publikováno v:
PLoS Computational Biology, Vol 13, Iss 4, p e1005463 (2017)
The flipping-out of a DNA base from the double helical structure is a key step of many cellular processes, such as DNA replication, modification and repair. Base pair opening is the first step of base flipping and the exact mechanism is still not wel
Externí odkaz:
https://doaj.org/article/d889cb339bd54d6b984ffb38cfb7caa6
Autor:
Christine S Schwaiger, Sara I Börjesson, Berk Hess, Björn Wallner, Fredrik Elinder, Erik Lindahl
Publikováno v:
PLoS ONE, Vol 7, Iss 10, p e45880 (2012)
The gating of voltage-gated ion channels is controlled by the arginine-rich S4 helix of the voltage-sensor domain moving in response to an external potential. Recent studies have suggested that S4 moves in three to four steps to open the conducting p
Externí odkaz:
https://doaj.org/article/243cd20f760a4ee8984e488beb5983b9
Skin permeability prediction with MD simulation sampling spatial and alchemical reaction coordinates
Publikováno v:
Biophysical Journal. 121:3837-3849
A molecular-level understanding of skin permeation may rationalize and streamline product development, and improve quality and control, of transdermal and topical drug delivery systems. It may also facilitate toxicity and safety assessment of cosmeti
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::df265287f0bd0842255b88e2faa8deae
https://doi.org/10.1016/j.bpj.2022.09.009
https://doi.org/10.1016/j.bpj.2022.09.009
Publikováno v:
Journal of Chemical Theory and Computation. 18:6134-6147
Various approaches have been proposed to include the effect of pH in molecular dynamics (MD) simulations. Among these, the λ-dynamics approach proposed by Brooks and co-workers [Kong, X.; Brooks III, C. L. J. Chem. Phys.1996, 105, 2414−2423] can b
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::da331f805a41829c439648ad22eeeaf0
https://doi.org/10.1021/acs.jctc.2c00517
https://doi.org/10.1021/acs.jctc.2c00517
Full documentation for the GROMACS 2022.6 patch release version.
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::adbd0325859ce0615781b3f19610e906
In this webinar we will give an overview of the new features that have been included in the recently released 2023 version of GROMACS. We will present many improvements related to performance on GPUs, in particular a new SYCL backend targeting AMD an
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0b0bcc6825d6c052c37882fd5cfc1e8c
Autor:
Mark Abraham, Andrey Alekseenko, Cathrine Bergh, Christian Blau, Eliane Briand, Mahesh Doijade, Stefan Fleischmann, Vytautas Gapsys, Gaurav Garg, Sergey Gorelov, Gilles Gouaillardet, Alan Gray, M. Eric Irrgang, Farzaneh Jalalypour, Joe Jordan, Christoph Junghans, Prashanth Kanduri, Sebastian Keller, Carsten Kutzner, Justin A. Lemkul, Magnus Lundborg, Pascal Merz, Vedran Miletić, Dmitry Morozov, Szilárd Páll, Roland Schulz, Michael Shirts, Alexey Shvetsov, Bálint Soproni, David van der Spoel, Philip Turner, Carsten Uphoff, Alessandra Villa, Sebastian Wingbermühle, Artem Zhmurov, Paul Bauer, Berk Hess, Erik Lindahl
Full documentation for the GROMACS 2023.1 release version.
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::9d039b18159e427c813181695d764b9a