Zobrazeno 1 - 10
of 61
pro vyhledávání: '"Stefan Boresch"'
Publikováno v:
Frontiers in Molecular Biosciences, Vol 9 (2022)
We present the software package transformato for the setup of large-scale relative binding free energy calculations. Transformato is written in Python as an open source project (https://github.com/wiederm/transformato); in contrast to comparable tool
Externí odkaz:
https://doaj.org/article/37be5c662e234375872c7476cc7f90ac
Publikováno v:
Molecules, Vol 28, Iss 10, p 4006 (2023)
Non-equilibrium work switching simulations and Jarzynski’s equation are a reliable method for computing free energy differences, ΔAlow→high, between two levels of theory, such as a pure molecular mechanical (MM) and a quantum mechanical/molecula
Externí odkaz:
https://doaj.org/article/82e4b77102ac4e5487edb343c26a4046
Publikováno v:
Molecules, Vol 24, Iss 4, p 681 (2019)
Indirect (S)QM/MM free energy simulations (FES) are vital to efficiently incorporating sufficient sampling and accurate (QM) energetic evaluations when estimating free energies of practical/experimental interest. Connecting between levels of theory,
Externí odkaz:
https://doaj.org/article/fa2cbec48d9346f6b6b12f4391818df8
Autor:
Benjamin T Miller, Rishi P Singh, Vinushka Schalk, Yuri Pevzner, Jingjun Sun, Carrie S Miller, Stefan Boresch, Toshiko Ichiye, Bernard R Brooks, H Lee Woodcock
Publikováno v:
PLoS Computational Biology, Vol 10, Iss 7, p e1003719 (2014)
This article describes the development, implementation, and use of web-based "lessons" to introduce students and other newcomers to computer simulations of biological macromolecules. These lessons, i.e., interactive step-by-step instructions for perf
Externí odkaz:
https://doaj.org/article/935989558a1943f4a9b1b42de82854d2
Autor:
Sara Tkaczyk, Johannes Karwounopoulos, Andreas Schöller, H. Lee Woodcock, Thierry Langer, Stefan Boresch, Marcus Wieder
To achieve chemical accuracy in free energy calculations, it is necessary to accurately describe the system's potential energy surface and efficiently sample configurations from its Boltzmann distribution. While neural network potentials (NNPs) have
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::d93aea4201d10609dcce9802788283b5
https://doi.org/10.26434/chemrxiv-2023-qq206
https://doi.org/10.26434/chemrxiv-2023-qq206
Nonequilibrium work switching simulations and Jarzynski’s equation are a reliable method to compute free energy differences, ΔAlow→high, between two levels of theory, such as a pure molecular mechanical (MM) and a quantum mechanical/molecular me
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::32b3c4f29274dbeb2ba026db7297a083
https://doi.org/10.20944/preprints202303.0483.v1
https://doi.org/10.20944/preprints202303.0483.v1
Publikováno v:
The Journal of Physical Chemistry B. 126:2798-2811
A key step during indirect alchemical free energy simulations using quantum mechanical/molecular mechanical (QM/MM) hybrid potential energy functions is the calculation of the free energy difference Δ
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0055b646e0bedf77fa3f98bb65fdf817
https://doi.org/10.1021/acs.jpcb.2c00696
https://doi.org/10.1021/acs.jpcb.2c00696
Publikováno v:
Journal of Chemical Theory and Computation
In calculations of relative free energy differences, the number of atoms of the initial and final states is rarely the same. This necessitates the introduction of dummy atoms. These placeholders interact with the physical system only by bonded energy
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5be33a2ca793e4f22dcd6faad5d45f5c
https://doi.org/10.1021/acs.jctc.0c01328
https://doi.org/10.1021/acs.jctc.0c01328
Publikováno v:
Journal of computational chemistry. 43(17)
We describe the theory of the so-called common-core/serial-atom-insertion (CC/SAI) approach to compute alchemical free energy differences and its practical implementation in a Python package called Transformato. CC/SAI is not tied to a specific biomo
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e904fed0ea247d04b0bc74fb2607ec75
https://pubmed.ncbi.nlm.nih.gov/35485139
https://pubmed.ncbi.nlm.nih.gov/35485139
Publikováno v:
Journal of Chemical Theory and Computation. 15:4632-4645
The use of the most accurate (i.e., QM or QM/MM) levels of theory for free energy simulations (FES) is typically not possible. Primarily, this is because the computational cost associated with the extensive configurational sampling needed for converg
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::0097ce5ab834182e198a550cfeb73dc1
https://doi.org/10.1021/acs.jctc.9b00084
https://doi.org/10.1021/acs.jctc.9b00084