Demonstration venue · read-only. Every page can be browsed; the buttons that would change it are switched off. Create an account to run TaxoReview on your own data. A simulation from public publication records: the people listed were not invited and did not agree to review.
? Tutorial for this page

Prasun Kumar

dblp:124/9329 · DBLP profile ↗
← Back
1ranked-venue papers
1as first author
1since 2021 · last 2021
0000-0002-2008-3347ORCID · reported

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1 · 1 first-author · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%

Topics — the 3 heaviest of 4, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › structural bioinformatics › structural motif analysis
helix packing geometry
0.512021
Socket2: a program for locating, visualizing and analyzing coiled-coil interfaces in protein structures · Bioinform. 2021
Bioinformatics and computational biology
protein structure analysis
0.512021
Socket2: a program for locating, visualizing and analyzing coiled-coil interfaces in protein structures · Bioinform. 2021
Bioinformatics and computational biology › structural bioinformatics › protein structure representation
protein structure visualization
0.112021
Socket2: a program for locating, visualizing and analyzing coiled-coil interfaces in protein structures · Bioinform. 2021

Methods — techniques the papers use, named apart from their topics

knobs-into-holes packing analysis · 0.5
YearPublicationVenuePosition
2021 Socket2: a program for locating, visualizing and analyzing coiled-coil interfaces in protein structures
abstract
MOTIVATION: Protein-protein interactions are central to all biological processes. One frequently observed mode of such interactions is the α-helical coiled coil (CC). Thus, an ability to extract, visualize and analyze CC interfaces quickly and without expert guidance would facilitate a wide range of biological research. In 2001, we reported Socket, which locates and characterizes CCs in protein structures based on the knobs-into-holes (KIH) packing between helices in CCs. Since then, studies of natural and de novo designed CCs have boomed, and the number of CCs in the RCSB PDB has increased rapidly. Therefore, we have updated Socket and made it accessible to expert and nonexpert users alike. RESULTS: The original Socket only classified CCs with up to six helices. Here, we report Socket2, which rectifies this oversight to identify CCs with any number of helices, and KIH interfaces with any of the 20 proteinogenic residues or incorporating nonnatural amino acids. In addition, we have developed a new and easy-to-use web server with additional features. These include the use of NGL Viewer for instantly visualizing CCs, and tabs for viewing the sequence repeats, helix-packing angles and core-packing geometries of CCs identified and calculated by Socket2. AVAILABILITY AND IMPLEMENTATION: Socket2 has been tested on all modern browsers. It can be accessed freely at http://coiledcoils.chm.bris.ac.uk/socket2/home.html. The source code is distributed using an MIT licence and available to download under the Downloads tab of the Socket2 home page.
Prasun Kumar, Derek N. Woolfson
Bioinform.1