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Filippo Boscariol

dblp:64/9844 · DBLP profile ↗
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1ranked-venue papers
0as first author
0since 2021 · last 2011
—ORCID · none

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

Applied, interdisciplinary, general and emerging computing · 1

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 3, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology
protein structure analysis
0.112011
RING: networking interacting residues, evolutionary information and energetics in protein structures · Bioinform. 2011
Bioinformatics and computational biology › structural bioinformatics › protein structure representation
residue interaction network
0.112011
RING: networking interacting residues, evolutionary information and energetics in protein structures · Bioinform. 2011
Bioinformatics and computational biology › structural bioinformatics › protein structure representation
protein structure visualization
0.012011
RING: networking interacting residues, evolutionary information and energetics in protein structures · Bioinform. 2011

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

network topology analysis · 0.1graph theory · 0.1
YearPublicationVenuePosition
2011 RING: networking interacting residues, evolutionary information and energetics in protein structures
abstract
MOTIVATION: Residue interaction networks (RINs) have been used in the literature to describe the protein 3D structure as a graph where nodes represent residues and edges physico-chemical interactions, e.g. hydrogen bonds or van-der-Waals contacts. Topological network parameters can be calculated over RINs and have been correlated with various aspects of protein structure and function. Here we present a novel web server, RING, to construct physico-chemically valid RINs interactively from PDB files for subsequent visualization in the Cytoscape platform. The additional structure-based parameters secondary structure, solvent accessibility and experimental uncertainty can be combined with information regarding residue conservation, mutual information and residue-based energy scoring functions. Different visualization styles are provided to facilitate visualization and standard plugins can be used to calculate topological parameters in Cytoscape. A sample use case analyzing the active site of glutathione peroxidase is presented. AVAILABILITY: The RING server, supplementary methods, examples and tutorials are available for non-commercial use at URL: http://protein.bio.unipd.it/ring/.
Alberto J. M. Martin, Michele Vidotto, Filippo Boscariol, Tomás Di Domenico, Ian Walsh, Silvio C. E. Tosatto
Bioinform.3