Zobrazeno 1 - 9
of 9
pro vyhledávání: '"Noah S. Bieler"'
Publikováno v:
PLoS Computational Biology, Vol 8, Iss 10, p e1002692 (2012)
The pre-fibrillar stages of amyloid formation have been implicated in cellular toxicity, but have proved to be challenging to study directly in experiments and simulations. Rational strategies to suppress the formation of toxic amyloid oligomers requ
Externí odkaz:
https://doaj.org/article/b0b92e549d49468ca71606453f614e20
Publikováno v:
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
An algorithm is proposed for performing molecular dynamics (MD) simulations of a biomolecular solute represented at atomistic resolution surrounded by a surface layer of atomistic fine-grained (FG) solvent molecules within a bulk represented by coars
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0a81c1dc3733e1586760a9fe87201797
https://doi.org/10.1021/acs.jctc.5b00406
https://doi.org/10.1021/acs.jctc.5b00406
Publikováno v:
Journal of Computational Chemistry. 36:1686-1697
In a recent article (Bieler et al., J. Chem. Theory Comput. 2014, 10, 3006), we introduced a combination of λ-dynamics and local-elevation umbrella-sampling termed λ-LEUS to calculate free-energy changes associated with alchemical processes using m
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fe3dc0209b17dd6caeac372e26b51b23
https://doi.org/10.1002/jcc.23984
https://doi.org/10.1002/jcc.23984
Publikováno v:
Journal of Chemical Theory and Computation
When using molecular dynamics (MD) simulations for the calculation of alchemical free energy changes the extended dynamics method called ? dynamics (?D) in its currently available implementations does not compare very favorably with thermodynamic int
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e79422ba1f2e95a9440dcaf4752ae39f
Analysis of the Cartesian Tensor Transfer Method for Calculating Vibrational Spectra of Polypeptides
Publikováno v:
Journal of Chemical Theory and Computation. 7:1867-1881
The Cartesian Tensor Transfer Method (CTTM) was proposed as an efficient way to calculate infrared, Raman, and Raman Optical Activity (ROA) spectra for large molecules from the Hessian matrix and property tensor derivatives calculated for smaller mol
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f6acc8c79818c7412a93d726b92c6081
https://doi.org/10.1021/ct2001478
https://doi.org/10.1021/ct2001478
Publikováno v:
Journal of chemical theory and computation. 11(6)
An extension of the λ-local-elevation umbrella-sampling (λ-LEUS) scheme [ Bieler et al. J. Chem. Theory Comput. 2014 , 10 , 3006 ] is proposed to handle the multistate (MS) situation, i.e. the calculation of the relative free energies of multiple p
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::60220cc175d0777ff343ad97153d521c
https://pubmed.ncbi.nlm.nih.gov/26575556
https://pubmed.ncbi.nlm.nih.gov/26575556
Publikováno v:
PLoS Computational Biology
PLoS Computational Biology, Vol 8, Iss 10, p e1002692 (2012)
PLoS Computational Biology, 8 (10)
PLoS Computational Biology, Vol 8, Iss 10, p e1002692 (2012)
PLoS Computational Biology, 8 (10)
The pre-fibrillar stages of amyloid formation have been implicated in cellular toxicity, but have proved to be challenging to study directly in experiments and simulations. Rational strategies to suppress the formation of toxic amyloid oligomers requ
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7954126a6aa27229fff92072d99175e8
https://pubmed.ncbi.nlm.nih.gov/23071427
https://pubmed.ncbi.nlm.nih.gov/23071427
Publikováno v:
The Journal of Chemical Physics. 142:165102
Estimating the relative stabilities of different conformational states of a (bio-)molecule using molecular dynamics simulations involves two challenging problems: the conceptual problem of how to define the states of interest and the technical proble
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ab3afc4820b3f03c647c6d8ac6278c7e
https://doi.org/10.1063/1.4918548
https://doi.org/10.1063/1.4918548
Publikováno v:
The Journal of Chemical Physics. 141:201101
In a recent article [Bieler et al., J. Chem. Theory Comput. 10, 3006-3022 (2014)], we introduced a combination of the λ-dynamics (λD) approach for calculating alchemical free-energy differences and of the local-elevation umbrella-sampling (LEUS) me
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0afd54427ed1488d967a16e7e4617a16
https://doi.org/10.1063/1.4902361
https://doi.org/10.1063/1.4902361