UCSF Chimera [1] is a widely used software for the visualization and modeling of protein 3D structures. We developed two extensions which support the analysis of protein variants and protein engineering. <\/p>\n
The first extension offers an interface to our online service MAESTRO<\/a> [2], a versatile tool for the prediction of stability changes upon point mutations. The extension provides access to the most popular application scenarios. <\/p>\n The second extension performs multiple structure alignments (MStAs) by utilizing our web service PIRATES [3]. PIRATES is a meta server for MStAs, which currently provides access to eight widely used alignment methods. In addition, the service computes a consensus alignment based on their results.<\/p>\n Both extensions are written in Python and communicate with our RESTful web service called BioDApps [4]. All components are freely available for academic research and do not have any dependencies other than a UCSF Chimera (version 11.1 or later) installation and an internet connection.<\/p>\n The extensions are free for non-commercial use. By using this software, you accept the terms of the License Agreement<\/a>. Please do not hesitate to contact us<\/a> in the case of any questions.<\/p>\n Version 0.8 beta<\/a><\/p>\n Unpack the zip file with your favorite packing tool and copy its content into the “share” directory of your UCSF Chimera installation. Open up Chimera and launch Tools> BioDApps> MAESTRO or Tools> BioDApps> PIRATES, respectively.<\/p>\n A user manual is not yet available but will be provided soon. Please do not hesitate to contact us<\/a> in the case of any questions. <\/p>\n [1] UCSF Chimera – a visualization system for exploratory research and analysis. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. J Comput Chem.<\/em> 2004 Oct;25(13):1605-12. PMID: 15264254<\/a><\/p>\n [2] MAESTRO – multi agent stability prediction upon point mutations. Laimer J, Hofer H, Fritz M, Wegenkittl S, Lackner P. BMC Bioinformatics<\/em> 2015, 16:116 doi:10.1186\/s12859-015-0548-6. PMID: 25885774<\/a><\/p>\n [3] PIRATES \u2013 Protein Structure Alignment Meta Server. Doblmann J, Haunschmid V, Holzmann H, St\u00fctz C, Laimer J, Lackner P. Poster, \u00d6GMBT Annual Meeting<\/em> 2012. link.<\/a><\/p>\n [4] BioDApps – Distributed Bioinformatics Applications. Bernwinkler T, Hiebl-Flach J, Katzenschlager J, K\u00f6berl D, Lengauer D, Nagl L, Schubert S, Laimer J, Lackner P. Poster, \u00d6GMBT Annual Meeting<\/em> 214. link.<\/a><\/p>\n","protected":false},"excerpt":{"rendered":" UCSF Chimera [1] is a widely used software for the visualization and modeling of protein 3D structures. We developed two extensions which support the analysis of protein variants and protein engineering. The first extension offers an interface to our online service MAESTRO [2], a versatile tool for the prediction of stability changes upon point mutations. … Continue reading UCSF Chimera Extensions<\/span> Download<\/h3>\n
Installation<\/h6>\n
Missing Features and Known Issues<\/h6>\n
References<\/h3>\n