Zobrazeno 1 - 10
of 173
pro vyhledávání: '"David van der Spoel"'
Autor:
Vytautas Gapsys, Ahmet Yildirim, Matteo Aldeghi, Yuriy Khalak, David van der Spoel, Bert L. de Groot
Publikováno v:
Communications Chemistry, Vol 4, Iss 1, Pp 1-13 (2021)
Molecular dynamics-based approaches to calculate absolute protein–ligand binding free energy often rely on equilibrium free energy perturbation (FEP) protocols. Here, the authors study ligands binding to bromodomains and T4 lysozyme and find that b
Externí odkaz:
https://doaj.org/article/53ecbf2eedd34149bc3dad8e7658da0f
Publikováno v:
Communications Chemistry, Vol 4, Iss 1, Pp 1-10 (2021)
Molten salt electrolytes are widely used in energy storage and conversion, but our understanding of conductivity trends remains incomplete. Here, computational approaches are used to determine ionic electrical mobilities, local structures, and kineti
Externí odkaz:
https://doaj.org/article/ed06946aef3b4087b37bbb2a86bc7aa8
Publikováno v:
ACS Omega, Vol 4, Iss 24, Pp 20654-20664 (2019)
Externí odkaz:
https://doaj.org/article/77352f42c24c44fc9645f8cf0dcc55bf
Publikováno v:
ACS Omega, Vol 4, Iss 9, Pp 13772-13781 (2019)
Externí odkaz:
https://doaj.org/article/049c8469e3f347c6927660105e08ba40
Publikováno v:
International Journal of Molecular Sciences, Vol 23, Iss 13, p 7313 (2022)
The human genome codes only a few thousand druggable proteins, mainly receptors and enzymes. While this pool of available drug targets is limited, there is an untapped potential for discovering new drug-binding mechanisms and modes. For example, enzy
Externí odkaz:
https://doaj.org/article/bdc63e91be1f4f86a203a8f95f8aff17
Publikováno v:
Journal of Cheminformatics, Vol 9, Iss 1, Pp 1-12 (2017)
Abstract Background Targets with multiple (prerequisite or allosteric) binding sites have an increasing importance in drug design. Experimental determination of atomic resolution structures of ligands weakly bound to multiple binding sites is often c
Externí odkaz:
https://doaj.org/article/6b2a57c644404f7f85497041e8973a54
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
Publikováno v:
Physical Review Research, Vol 2, Iss 3, p 033277 (2020)
The solvation free energy (SFE) is a key property in the thermodynamics of chemical processes. It can be evaluated using molecular simulations with good statistical accuracy. However, force field predictions exhibit systematic errors due to uncertain
Externí odkaz:
https://doaj.org/article/6fa10ed5e1144dbca8b8f2168e9f0aee
Autor:
Alexandr Nasedkin, Moreno Marcellini, Tomasz L Religa, Stefan M Freund, Andreas Menzel, Alan R Fersht, Per Jemth, David van der Spoel, Jan Davidsson
Publikováno v:
PLoS ONE, Vol 10, Iss 5, p e0125662 (2015)
The folding and unfolding of protein domains is an apparently cooperative process, but transient intermediates have been detected in some cases. Such (un)folding intermediates are challenging to investigate structurally as they are typically not long
Externí odkaz:
https://doaj.org/article/0c69037db4244bb1b1a87aca2faf107d
Publikováno v:
PLoS Computational Biology, Vol 8, Iss 5, p e1002502 (2012)
Dissolution of many plant viruses is thought to start with swelling of the capsid caused by calcium removal following infection, but no high-resolution structures of swollen capsids exist. Here we have used microsecond all-atom molecular simulations
Externí odkaz:
https://doaj.org/article/3f75d5b69eeb44088810a1658b49602d