ANCA: A Web Server for Amino Acid Networks Construction and Analysis
Amino acid network (AAN) models empower us to gain insights into protein structures and functions by describing a protein 3D structure as a graph, where nodes represent residues and edges as amino acid interactions. Here, we present the ANCA, an interactive Web server for Amino Acids Network Constru...
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doaj-175d0388b4c24a4c9103ea45c0f1de442020-11-25T04:11:22ZengFrontiers Media S.A.Frontiers in Molecular Biosciences2296-889X2020-11-01710.3389/fmolb.2020.582702582702ANCA: A Web Server for Amino Acid Networks Construction and AnalysisWenying Yan0Chunjiang Yu1Jiajia Chen2Jianhong Zhou3Bairong Shen4Center for Systems Biology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, ChinaSchool of Biotechnology, Suzhou Industrial Park Institute of Services Outsourcing, Suzhou, ChinaSchool of Chemistry, Biology and Materials Engineering, Suzhou University of Science and Technology, Suzhou, ChinaPublic Library of Science, San Francisco, CA, United StatesInstitutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, ChinaAmino acid network (AAN) models empower us to gain insights into protein structures and functions by describing a protein 3D structure as a graph, where nodes represent residues and edges as amino acid interactions. Here, we present the ANCA, an interactive Web server for Amino Acids Network Construction and Analysis based on a single structure or a set of structures from the Protein Data Bank. The main purpose of ANCA is to provide a portal for three types of an environment-dependent residue contact energy (ERCE)-based network model, including amino acid contact energy network (AACEN), node-weighted amino acid contact energy network (NACEN), and edge-weighted amino acid contact energy network (EACEN). For comparison, the C-alpha distance-based network model is also included, which can be extended to protein–DNA/RNA complexes. Then, the analyses of different types of AANs were performed and compared from node, edge, and network levels. The network and corresponding structure can be visualized directly in the browser. The ANCA enables researchers to investigate diverse concerns in the framework of AAN, such as the interpretation of allosteric regulation and functional residues. The ANCA portal, together with an extensive help, is available at http://sysbio.suda.edu.cn/anca/.https://www.frontiersin.org/articles/10.3389/fmolb.2020.582702/fullAmino acids networkANCA portalnetwork analysisprotein structureallosteric regulationfunctional residues |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Wenying Yan Chunjiang Yu Jiajia Chen Jianhong Zhou Bairong Shen |
spellingShingle |
Wenying Yan Chunjiang Yu Jiajia Chen Jianhong Zhou Bairong Shen ANCA: A Web Server for Amino Acid Networks Construction and Analysis Frontiers in Molecular Biosciences Amino acids network ANCA portal network analysis protein structure allosteric regulation functional residues |
author_facet |
Wenying Yan Chunjiang Yu Jiajia Chen Jianhong Zhou Bairong Shen |
author_sort |
Wenying Yan |
title |
ANCA: A Web Server for Amino Acid Networks Construction and Analysis |
title_short |
ANCA: A Web Server for Amino Acid Networks Construction and Analysis |
title_full |
ANCA: A Web Server for Amino Acid Networks Construction and Analysis |
title_fullStr |
ANCA: A Web Server for Amino Acid Networks Construction and Analysis |
title_full_unstemmed |
ANCA: A Web Server for Amino Acid Networks Construction and Analysis |
title_sort |
anca: a web server for amino acid networks construction and analysis |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Molecular Biosciences |
issn |
2296-889X |
publishDate |
2020-11-01 |
description |
Amino acid network (AAN) models empower us to gain insights into protein structures and functions by describing a protein 3D structure as a graph, where nodes represent residues and edges as amino acid interactions. Here, we present the ANCA, an interactive Web server for Amino Acids Network Construction and Analysis based on a single structure or a set of structures from the Protein Data Bank. The main purpose of ANCA is to provide a portal for three types of an environment-dependent residue contact energy (ERCE)-based network model, including amino acid contact energy network (AACEN), node-weighted amino acid contact energy network (NACEN), and edge-weighted amino acid contact energy network (EACEN). For comparison, the C-alpha distance-based network model is also included, which can be extended to protein–DNA/RNA complexes. Then, the analyses of different types of AANs were performed and compared from node, edge, and network levels. The network and corresponding structure can be visualized directly in the browser. The ANCA enables researchers to investigate diverse concerns in the framework of AAN, such as the interpretation of allosteric regulation and functional residues. The ANCA portal, together with an extensive help, is available at http://sysbio.suda.edu.cn/anca/. |
topic |
Amino acids network ANCA portal network analysis protein structure allosteric regulation functional residues |
url |
https://www.frontiersin.org/articles/10.3389/fmolb.2020.582702/full |
work_keys_str_mv |
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