Result: PCN-Miner: an open-source extensible tool for the analysis of Protein Contact Networks.

Title:
PCN-Miner: an open-source extensible tool for the analysis of Protein Contact Networks.
Authors:
Guzzi PH; Department of Surgical and Medical Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy., Di Paola L; Unit of Chemical-Physics Fundamentals in Chemical Engineering, Department of Engineering, Università Campus Bio-Medico di Roma, 00128 Rome, Italy., Giuliani A; Environment and Health Department, Istituto Superiore di Sanità, 00161Rome, Italy., Veltri P; Department of Surgical and Medical Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy.
Source:
Bioinformatics (Oxford, England) [Bioinformatics] 2022 Sep 02; Vol. 38 (17), pp. 4235-4237.
Publication Type:
Journal Article; Research Support, Non-U.S. Gov't
Language:
English
Journal Info:
Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE
Imprint Name(s):
Original Publication: Oxford : Oxford University Press, c1998-
MeSH Terms:
Proteins* , Protein Interaction Mapping*, Humans ; Programming Languages ; SARS-CoV-2 ; Software
Grant Information:
PON-VQA
Substance Nomenclature:
0 (Proteins)
0 (spike protein, SARS-CoV-2)
EC 3.4.17.23 (ACE2 protein, human)
Entry Date(s):
Date Created: 20220708 Date Completed: 20221115 Latest Revision: 20221222
Update Code:
20250114
DOI:
10.1093/bioinformatics/btac450
PMID:
35799364
Database:
MEDLINE

Further Information

Motivation: Protein Contact Network (PCN) is a powerful method for analysing the structure and function of proteins, with a specific focus on disclosing the molecular features of allosteric regulation through the discovery of modular substructures. The importance of PCN analysis has been shown in many contexts, such as the analysis of SARS-CoV-2 Spike protein and its complexes with the Angiotensin Converting Enzyme 2 (ACE2) human receptors. Even if there exist many software tools implementing such methods, there is a growing need for the introduction of tools integrating existing approaches.
Results: We present PCN-Miner, a software tool implemented in the Python programming language, able to (i) import protein structures from the Protein Data Bank; (ii) generate the corresponding PCN; (iii) model, analyse and visualize PCNs and related protein structures by using a set of known algorithms and metrics. The PCN-Miner can cover a large set of applications: from clustering to embedding and subsequent analysis.
Availability and Implementation: The PCN-Miner tool is freely available at the following GitHub repository: https://github.com/hguzzi/ProteinContactNetworks. It is also available in the Python Package Index (PyPI) repository.
(© The Author(s) 2022. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)