Zobrazeno 1 - 10
of 44
pro vyhledávání: '"Hari S. Muddana"'
Autor:
Lee-Ping Wang, Michael K. Gilson, Sophie M Kantonen, Hari S. Muddana, Niel M. Henriksen, Michael Schauperl
Publikováno v:
Journal of chemical theory and computation, vol 16, iss 2
Molecular dynamics simulations are helpful tools for a range of applications, ranging from drug discovery to protein structure determination. The successful use of this technology largely depends on the potential function, or force field, used to det
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::44e111c486ec017d1534df7b582a107c
https://doi.org/10.1021/acs.jctc.9b00713
https://doi.org/10.1021/acs.jctc.9b00713
Publikováno v:
PLoS ONE, Vol 9, Iss 12, p e113119 (2014)
Many biomolecules have machine-like functions, and accordingly are discussed in terms of mechanical properties like force and motion. However, the concept of stress, a mechanical property that is of fundamental importance in the study of macroscopic
Externí odkaz:
https://doaj.org/article/a45c2de6c9a94be39a5a442307e31db4
We utilize a previously described Minimal Basis Iterative Stockholder (MBIS) method to carry out an atoms-in-molecules partitioning of electron densities. Information from these atomic densities is then mapped to Lennard-Jones parameters using a set
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::657bc6572aa8b5a041d20854a94ccc41
https://doi.org/10.26434/chemrxiv.9121367.v1
https://doi.org/10.26434/chemrxiv.9121367.v1
Microscopic in situ measurements of the mechanical properties of lipid bilayers were derived from the mean and variance of the fluorescence lifetime distributions of 1’-dioctadecyl-3,3,3’3’-tetramethylindocarbocyanine perchlorate (DiI). In this
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::43522293bbdf60fb5e5966332e62b3c3
We report a water model, Bind3P (Version 0.1), which was obtained by using sensitivity analysis to readjust the Lennard-Jones parameters of the TIP3P model against experimental binding free energies for six host–guest systems, along with pure liqui
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::870b7f05eedf2c1c82315d5ff9b93a36
https://europepmc.org/articles/PMC6039243/
https://europepmc.org/articles/PMC6039243/
We report a water model, Bind3P (Version 0.1), which was obtained by using sensitivity analysis to readjust the Lennard-Jones parameters of the TIP3P model against experimental binding free energies for six host-guest systems, along with pure liquid
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bba8ffd28f1134c94957d686ae78de6c
https://doi.org/10.26434/chemrxiv.5848113.v2
https://doi.org/10.26434/chemrxiv.5848113.v2
We report a water model, Bind3P (Version 0.1), which was obtained by using sensitivity analysis to readjust the Lennard-Jones parameters of the TIP3P model against experimental binding free energies for six host-guest systems, along with pure liquid
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::d1a51f5ea20f0beae3d19f1e7e76608e
https://doi.org/10.26434/chemrxiv.5848113.v1
https://doi.org/10.26434/chemrxiv.5848113.v1
Autor:
Peter J. Butler, Ye Fang, Daniel Ahmed, Adem Ozcelik, Andreas Manz, Mengqian Lu, Tony Jun Huang, Stephen J. Benkovic, Jarrod B. French, Hari S. Muddana
Publikováno v:
Analytical Chemistry
Eliciting a cellular response to a changing chemical microenvironment is central to many biological processes including gene expression, cell migration, differentiation, apoptosis, and intercellular signaling. The nature and scope of the response is
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e10a95867a7ff133bb6ca438e6cc9a04
https://doi.org/10.1021/ac5033676
https://doi.org/10.1021/ac5033676
Publikováno v:
Journal of Chemical Theory and Computation
We used microsecond time scale molecular dynamics simulations to compute, at high precision, binding enthalpies for cucurbit[7]uril (CB7) with eight guests in aqueous solution. The results correlate well with experimental data from previously publish
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::206959cfc7d7efdd48d3d94286831a58
http://europepmc.org/articles/PMC4159218
http://europepmc.org/articles/PMC4159218
Publikováno v:
Journal of Chemical Theory and Computation
Quantum mechanical (QM) calculations of noncovalent interactions are uniquely useful as tools to test and improve molecular mechanics force fields and to model the forces involved in biomolecular binding and folding. Because the more computationally
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::691e43d6cd5c70e9c1d40f8056eaba3a
https://doi.org/10.1021/ct401111c
https://doi.org/10.1021/ct401111c