Zobrazeno 1 - 10
of 18
pro vyhledávání: '"Eli Hershkovits"'
Publikováno v:
PLoS ONE, Vol 10, Iss 5, p e0127034 (2015)
Steered Molecular Dynamics (SMD) has been seen to provide the potential of mean force (PMF) along a peptide unfolding pathway effectively but at significant computational cost, particularly in all-atom solvents. Adaptive steered molecular dynamics (A
Externí odkaz:
https://doaj.org/article/1b9518ab1a0a462f92503e9c258407d6
Autor:
Anton S Petrov, Chad R Bernier, Burak Gulen, Chris C Waterbury, Eli Hershkovits, Chiaolong Hsiao, Stephen C Harvey, Nicholas V Hud, George E Fox, Roger M Wartell, Loren Dean Williams
Publikováno v:
PLoS ONE, Vol 9, Iss 2, p e88222 (2014)
Accurate secondary structures are important for understanding ribosomes, which are extremely large and highly complex. Using 3D structures of ribosomes as input, we have revised and corrected traditional secondary (2°) structures of rRNAs. We identi
Externí odkaz:
https://doaj.org/article/753e7f655e844b92ae3b749e03d9e869
Publikováno v:
Journal of Chemical Theory and Computation. 12:2028-2037
Mechanically driven unfolding is a useful computational tool for extracting the energetics and stretching pathway of peptides. In this work, two representative β-hairpin peptides, chignolin (PDB: 1UAO ) and trpzip1 (PDB: 1LE0 ), were investigated us
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::412e960c2efaf3f7a9ca2d869ec5faaa
https://doi.org/10.1021/acs.jctc.5b01110
https://doi.org/10.1021/acs.jctc.5b01110
Autor:
Zachary Wartell, Jessica C. Bowman, Fengbo Li, Larry Freil, Chris C. Waterbury, Chad R. Bernier, Chiaolong Hsiao, Eli Hershkovits, James Jett, Anton S. Petrov, Stephen C. Harvey, Xiao Xiong, Martha A. Grover, Blacki Li Rudi Migliozzi, Lan Wang, Yuzhen Xue, Loren Dean Williams
Publikováno v:
Faraday Discuss.. 169:195-207
RiboVision is a visualization and analysis tool for the simultaneous display of multiple layers of diverse information on primary (1D), secondary (2D), and three-dimensional (3D) structures of ribosomes. The ribosome is a macromolecular complex conta
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::37fc10e68f1087233faaad14493a3d49
https://doi.org/10.1039/c3fd00126a
https://doi.org/10.1039/c3fd00126a
Autor:
Chiaolong Hsiao, Yuzhen Xue, Roger M. Wartell, Nicholas V. Hud, Stephen C. Harvey, Victor G. Stepanov, Anton S. Petrov, Chris C. Waterbury, Martha A. Grover, Eric A. Gaucher, George E. Fox, Eli Hershkovits, Loren Dean Williams, Chad R. Bernier
Publikováno v:
Nucleic Acids Research
We present a de novo re-determination of the secondary (2°) structure and domain architecture of the 23S and 5S rRNAs, using 3D structures, determined by X-ray diffraction, as input. In the traditional 2° structure, the center of the 23S rRNA is an
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::080721c7ba16b05d6e42e4fc6f326e83
http://europepmc.org/articles/PMC3753638
http://europepmc.org/articles/PMC3753638
Publikováno v:
IEEE/ACM Transactions on Computational Biology and Bioinformatics. 8:1604-1619
The local conformation of RNA molecules is an important factor in determining their catalytic and binding properties. The analysis of such conformations is particularly difficult due to the large number of degrees of freedom, such as the measured tor
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6c8a5b0965e828830459454ae6b08e61
https://doi.org/10.1109/tcbb.2010.128
https://doi.org/10.1109/tcbb.2010.128
Publikováno v:
The Journal of Physical Chemistry B. 112:5317-5326
In this paper, we have developed a geometric-based scaling model that describes the adsorption of diblock copolymer chains from good solvents and theta-solvents onto reactive surfaces of varying curvatures. To evaluate the impact of particle size on
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::40cebf768a0ac366a1d84ef9e7c733fb
https://doi.org/10.1021/jp7097894
https://doi.org/10.1021/jp7097894
Autor:
David S. Richardson, Laura Weston Murray, Jane S. Richardson, Loren Dean Williams, Daniela Ham, Kevin S. Keating, Jeffrey J. Headd, Eli Hershkovits, Anna Marie Pyle, Bohdan Schneider, R.M. Immormino, Gary J. Kapral, Helen M. Berman, John D. Westbrook, David Micallef
Publikováno v:
RNA. 14:465-481
A consensus classification and nomenclature are defined for RNA backbone structure using all of the backbone torsion angles. By a consensus of several independent analysis methods, 46 discrete conformers are identified as suitably clustered in a qual
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5b361ad5031502b118fac85961269e9e
https://doi.org/10.1261/rna.657708
https://doi.org/10.1261/rna.657708
Autor:
Chris C. Waterbury, Loren Dean Williams, Burak Gulen, Stephen C. Harvey, Nicholas V. Hud, Chiaolong Hsiao, George E. Fox, Chad R. Bernier, Anton S. Petrov, Eli Hershkovits, Roger M. Wartell
Publikováno v:
PLoS ONE
PLoS ONE, Vol 9, Iss 2, p e88222 (2014)
PLoS ONE, Vol 9, Iss 2, p e88222 (2014)
Accurate secondary structures are important for understanding ribosomes, which are extremely large and highly complex. Using 3D structures of ribosomes as input, we have revised and corrected traditional secondary (2°) structures of rRNAs. We identi
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::03aee2d870e5ac1b6fcdabc5d7d7f947
http://europepmc.org/articles/PMC3914948
http://europepmc.org/articles/PMC3914948
Publikováno v:
The journal of physical chemistry. C, Nanomaterials and interfaces. 111(33)
In this article, we have developed a simple model that describes the adsorption of polymer chains from a solution having a good solvent onto a reactive surface of varying curvatures. In order to evaluate the impact of particle size on the adsorption
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4c5e8a72dd770807aa5b9932bbf76137
https://pubmed.ncbi.nlm.nih.gov/23710263
https://pubmed.ncbi.nlm.nih.gov/23710263