scholarly journals Web-Based Computational Chemistry Education with CHARMMing II: Coarse-Grained Protein Folding

2014 ◽  
Vol 10 (7) ◽  
pp. e1003738 ◽  
Author(s):  
Frank C. Pickard ◽  
Benjamin T. Miller ◽  
Vinushka Schalk ◽  
Michael G. Lerner ◽  
H. Lee Woodcock ◽  
...  
2014 ◽  
Vol 10 (7) ◽  
pp. e1003719 ◽  
Author(s):  
Benjamin T. Miller ◽  
Rishi P. Singh ◽  
Vinushka Schalk ◽  
Yuri Pevzner ◽  
Jingjun Sun ◽  
...  

2014 ◽  
Vol 10 (7) ◽  
pp. e1003739 ◽  
Author(s):  
B. Scott Perrin ◽  
Benjamin T. Miller ◽  
Vinushka Schalk ◽  
H. Lee Woodcock ◽  
Bernard R. Brooks ◽  
...  

2019 ◽  
Author(s):  
Ruslan N. Tazhigulov ◽  
James R. Gayvert ◽  
Melissa Wei ◽  
Ksenia B. Bravaya

<p>eMap is a web-based platform for identifying and visualizing electron or hole transfer pathways in proteins based on their crystal structures. The underlying model can be viewed as a coarse-grained version of the Pathways model, where each tunneling step between hopping sites represented by electron transfer active (ETA) moieties is described with one effective decay parameter that describes protein-mediated tunneling. ETA moieties include aromatic amino acid residue side chains and aromatic fragments of cofactors that are automatically detected, and, in addition, electron/hole residing sites that can be specified by the users. The software searches for the shortest paths connecting the user-specified electron/hole source to either all surface-exposed ETA residues or to the user-specified target. The identified pathways are ranked based on their length. The pathways are visualized in 2D as a graph, in which each node represents an ETA site, and in 3D using available protein visualization tools. Here, we present the capability and user interface of eMap 1.0, which is available at https://emap.bu.edu.</p>


2012 ◽  
Vol 7 (4) ◽  
pp. 136-141
Author(s):  
I. Kalgin ◽  
Sergey Chekmarev

The problem of how a protein folds into its functional (native) state is one of the central problems of molecular biology, which attracts the attention of researchers from biology, physics and chemistry for many years. Of particular interest are general properties of the folding process, because the mechanisms of folding of different proteins can be essentially different. Previously, in the study of folding of fyn SH3 domain, we found that despite all the diversity and complexity of individual folding trajectories, the folding flows possess a well pronounced property of self-similarity, with a fractal character of the flow distributions. In the present paper, we study this phenomenon for another protein – beta3s, which is essentially different from the SH3 domain in its structure and folding kinetics. Also, in contrast to the fyn SH3 domain, for which a coarse-grained representation was used, we perform simulations on the atomic level of resolution. We show that the self-similarity and fractality of folding flows are observed is this case too, which suggests that these properties are characteristic of the protein folding dynamics


Author(s):  
S. Demurjian ◽  
H. Ren ◽  
S. Berhe ◽  
M. Devineni ◽  
Sushil Vegad ◽  
...  

Collaborative portals are emerging as a viable technology to allow groups of individuals to easily author, create, update, and share content via easy-to-use Web-based interfaces, for example, MediaWiki, Microsoft’s Sharepoint, and so forth. From a security perspective, these products are often limited and coarse grained in their authorization and authentication. For example, in a Wiki, the security model is often at two ends of the spectrum: anonymous users with no authorization and limited access via readonly browsing vs. registered users with full-range of access and limited oversight in content creation and modification. However, in practice, such full and unfettered access may not be appropriate for all users and for all applications, particularly as the collaborative technology moves into commercial usage (where copyright and intellectual property are vital) or sensitive domains such as healthcare (which ushave stringent HIPAA requirements). In this chapter, we report on our research and development effort of a role-based access control for collaborative Web portals that encompasses and realizes security at the application level, the document level (authoring and viewing), and the look-and-feel of the portal itself.


2020 ◽  
Vol 87 ◽  
pp. 107301
Author(s):  
Leandro Takeshi Hattori ◽  
Bruna Araujo Pinheiro ◽  
Rafael Bertolini Frigori ◽  
César Manuel Vargas Benítez ◽  
Heitor Silvério Lopes

2010 ◽  
Vol 5 (3) ◽  
pp. 217-240 ◽  
Author(s):  
Carlo Guardiani ◽  
Roberto Livi ◽  
Fabio Ce cconi

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