1,722,513 research outputs found
Mohammed-I-Sorour/COVID-19-main-protease: v1.0.0
No full textThis Work is presented as a contribution from the Matsika lab at Temple University, Philadelphia, Pennsylvania, to support the efforts against COVID-19.
In this repository I will describe the process we followed to prepare the COVID-6LU7 protein for docking
1-The 6lu7 protein was downloaded from the protein data bank: https://www.rcsb.org/structure/6LU7
2-The 6lu7 was crystallized in the presence of a covalently linked inhibitor, N3.
3-I removed the inhibitor and capped the Cys-145 residue sulfur atom with a hydrogen.
4-The the rest of the hydrogen of the system were added. the water molecule that came as a part of the crystallized structure were removed.
5-The most important step now is to relax the system after the removal of the covalently linked ligand. To do so, we ran 10ns equilibrium molecular dynamics to relax the system.
MD relaxation details: The protein topology was built using CHARMM36 FF while the positively charged ligand need a different treatment where we built its topology using CHARMM General Force Field (CGenFF)1. We solvated the system in a cubic simulation box using TIP3P waters and 150 M of NaCl. We ran the simulation at 310K and 1 atm in an NPT enesmble using the Leap-Frog integrator. We used the Particle Mesh Ewald for long-range electrostatics and Ewald cutoff distance of 15 angstroms. The simulation was ran for 50ns using GROMACS_2018.8.
I will provide the pdb files of the system at 4.8-ns (RMSD= 1.77 A)and 10-ns (RMSD= 3.28 A). The reason that I provide both of them is that the frame at 4.8 ns have been released earlier and is currently part of some research work. For future docking studies, I recommend using the 10 ns structure.
This work was done using the super computer system, HPC, of Temple University School of Science and Technology, Philadelphia, Pennsylvania. Aug 2020.
Please feel free to share any comments and or thoughts!!!
Best
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
- …
