dc.contributor.author | Aydınkal, Rasim Murat | |
dc.contributor.author | Serçinoğlu, Onur | |
dc.contributor.author | Özbek, Pemra | |
dc.date.accessioned | 2020-12-19T19:36:50Z | |
dc.date.available | 2020-12-19T19:36:50Z | |
dc.date.issued | 2019 | |
dc.identifier.citation | Aydınkal, R. M., Serçinoğlu, O., & Ozbek, P. (2019). ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism. Nucleic acids research, 47(W1), W471–W476. https://doi.org/10.1093/nar/gkz390 | en_US |
dc.identifier.issn | 0305-1048 | |
dc.identifier.issn | 1362-4962 | |
dc.identifier.uri | https://doi.org/10.1093/nar/gkz390 | |
dc.identifier.uri | https://hdl.handle.net/11436/1483 | |
dc.description | Sercinoglu, Onur/0000-0003-1361-8160; Ozbek, Pemra/0000-0002-3043-0015 | en_US |
dc.description | WOS: 000475901600068 | en_US |
dc.description | PubMed: 31114881 | en_US |
dc.description.abstract | ProSNEx (Protein Structure Network Explorer) is a web service for construction and analysis of Protein Structure Networks (PSNs) alongside amino acid flexibility, sequence conservation and annotation features. ProSNEx constructs a PSN by adding nodes to represent residues and edges between these nodes using user-specified interaction distance cutoffs for either carbon-alpha, carbon-beta or atom-pair contact networks. Different types of weighted networks can also be constructed by using either (i) the residue-residue interaction energies in the format returned by gRINN, resulting in a Protein Energy Network (PEN); (ii) the dynamical cross correlations from a coarse-grained Normal Mode Analysis (NMA) of the protein structure; (iii) interaction strength. Upon construction of the network, common network metrics (such as node centralities) as well as shortest paths between nodes and k-cliques are calculated. Moreover, additional features of each residue in the form of conservation scores and mutation/natural variant information are included in the analysis. By this way, tool offers an enhanced and direct comparison of network-based residue metrics with other types of biological information. ProSNEx is free and open to all users without login requirement at http://prosnex-tool.com. | en_US |
dc.language.iso | eng | en_US |
dc.publisher | Oxford Univ Press | en_US |
dc.rights | info:eu-repo/semantics/openAccess | en_US |
dc.subject | Molecular dynamics simulations | en_US |
dc.title | ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism | en_US |
dc.type | article | en_US |
dc.contributor.department | RTEÜ, Mühendislik ve Mimarlık Fakültesi, Biyomühendislik Bölümü | en_US |
dc.contributor.institutionauthor | Serçinoğlu, Onur | |
dc.identifier.doi | 10.1093/nar/gkz390 | |
dc.identifier.volume | 47 | en_US |
dc.identifier.issue | W1 | en_US |
dc.identifier.startpage | W471 | en_US |
dc.identifier.endpage | W476 | en_US |
dc.ri.edit | oa | en_US |
dc.relation.journal | Nucleic Acids Research | en_US |
dc.relation.publicationcategory | Makale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı | en_US |