Zobrazeno 1 - 9
of 9
pro vyhledávání: '"Yuriy Khalak"'
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:
Journal of Chemical Theory and Computation
Drug discovery can be thought as a search for a needle in a haystack. Finding the initial active hit molecules, the optimal decoration of lead molecule analogues, to final clinical candidate selection is an on-going trade-off between applying the bes
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7d2ef10287ab26e8cc98ce9503b138a9
https://hdl.handle.net/21.11116/0000-000C-0DAE-321.11116/0000-000C-0DB0-F
https://hdl.handle.net/21.11116/0000-000C-0DAE-321.11116/0000-000C-0DB0-F
Autor:
B. L. de Groot, David L. Mobley, Gary Tresadern, Yuriy Khalak, Hannah Magdalena Baumann, Matteo Aldeghi, Vytautas Gapsys
Publikováno v:
Chemical Science
The recent advances in relative protein–ligand binding free energy calculations have shown the value of alchemical methods in drug discovery. Accurately assessing absolute binding free energies, although highly desired, remains a challenging endeav
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9a6bbfdd845229534faa0443c059071e
https://doi.org/10.26434/chemrxiv-2021-rxxbb
https://doi.org/10.26434/chemrxiv-2021-rxxbb
Autor:
Pranav Madhikar, Bjoern Baumeier, Christoph Junghans, Onur Çaylak, Gianluca Tirimbo, Joshua Brown, Yuriy Khalak, Lothar Brombacher, Jens Wehner
Publikováno v:
Journal of Chemical Theory and Computation
Journal of Chemical Theory and Computation, 14(12), 6253-6268. American Chemical Society
Journal of Chemical Theory and Computation, 14(12), 6253-6268. American Chemical Society
Many-body Green's functions theory within the GW approximation and the Bethe-Salpeter Equation (BSE) is implemented in the open-source VOTCA-XTP software, aiming at the calculation of electronically excited states in complex molecular environments. B
Autor:
Bert L. de Groot, Yuriy Khalak, Ahmet Yildirim, Vytautas Gapsys, David van der Spoel, Matteo Aldeghi
Publikováno v:
Communications Chemistry
Communications Chemistry, Vol 4, Iss 1, Pp 1-13 (2021)
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 bot
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3c3459b28959204ee0610afba0ad7c2a
http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-445579
http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-445579
Publikováno v:
Journal of Chemical Physics, 149(22):224507. American Chemical Society
A new five point potential for liquid water, TIP5P/2018, is presented along with the techniques used to derive its charges from ab initio per-molecule electrostatic potentials in the liquid phase using the split charge equilibration (SQE) of Nistor e
Publikováno v:
Journal of Chemical Physics, 147(13):134108. American Chemical Society
Water is a notoriously difficult substance to model both accurately and efficiently. Here, we focus on descriptions with a single coarse-grained particle per molecule using the so-called approximate non-conformal and generalized Stockmayer potentials
Publikováno v:
Biochemistry. 50:8846-8852
Mandelate racemase (EC 5.1.2.2) from Pseudomonas putida catalyzes the interconversion of the enantiomers of mandelic acid and a variety of aryl- and heteroaryl-substituted mandelate derivatives, suggesting that β,γ-unsaturation is a requisite featu
Autor:
'Yuriy Khalak
Publikováno v:
Gary Tresadern