{"id":22,"date":"2013-08-08T12:58:27","date_gmt":"2013-08-08T16:58:27","guid":{"rendered":"http:\/\/research.chemistry.ohio-state.edu\/foster\/?page_id=22"},"modified":"2017-07-25T11:40:46","modified_gmt":"2017-07-25T15:40:46","slug":"software","status":"publish","type":"page","link":"https:\/\/research.cbc.osu.edu\/foster.281\/software\/","title":{"rendered":"Custom Software"},"content":{"rendered":"

Quick Links:<\/h1>\n

MESMER – Minimal Ensemble Solutions to Multiple Experimental Data<\/a>
\nGUARDD –\u00a0Graphical User-friendly Analysis of Relaxation Dispersion Data<\/a>
\nPyMOL OSU Site License Info<\/a><\/p>\n

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MESMER<\/a><\/h2>\n

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\"\"<\/a>Many (if not most) biological processes require structural, configurational, or compositional flexibility. DNA binding proteins, for example, are often highly flexible yet demonstrate only a few configurations that are functionally significant. Other systems frequently contain components that exist in multiple oligomeric states or assemblies, each with distinctly different behavior. Once such way of analyzing the averaged data obtained from such heterogeneous conditions is with a minimal ensemble, a collection of components that together are able to recapitulate the available experimental data.<\/p>\n

 <\/p>\n

MESMER (M<\/span>inimal E<\/span>nsemble S<\/span>olutions to M<\/span>ultiple E<\/span>xperimental R<\/span>estraints) seeks to assist researchers in analyzing the experimentally averaged data obtained from any number of experimental techniques. SAXS, NMR pseudocontact shifts, residual dipolar coupling, FRET, and DEER data, for example, can all be simultaneously fit by MESMER in order to provide the both the range of potential structures or to identify particularly prominent states of a given system. MESMER is easy to use, open source<\/a>, highly customizable, and comes with an array of tools to fit, analyze, and interpret the data and results from your system.<\/p>\n

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 <\/p>\n

GUARDD<\/a><\/h2>\n

\"GUARDD-SimRD-2011.06.24--06\"<\/a>Molecular dynamics are essential for life, and nuclear magnetic resonance (NMR) spectroscopy has been used extensively to characterize these phenomena since the 1950s. For the past 15\u00a0years, the Carr-Purcell Meiboom-Gill relaxation dispersion (CPMG RD) NMR experiment has afforded advanced NMR labs access to kinetic, thermodynamic, and structural details of protein and RNA dynamics in the crucial \u03bcs-ms time window. However, analysis of RD data is challenging because datasets are often large and require many non-linear fitting parameters, thereby confounding assessment of accuracy. Moreover, novice CPMG experimentalists face an additional barrier because current software options lack an intuitive user interface and extensive documentation.<\/p>\n

 <\/p>\n

We present the open-source software package GUARDD (Graphical User-friendly Analysis of Relaxation Dispersion Data), which is designed to organize, automate, and enhance the analytical procedures which operate on CPMG RD data (guardd-master.zip<\/a>). This MATLAB-based program includes a graphical user interface, permits global fitting to multi-field, multi-temperature, multi-coherence data, and implements\u00a0\u03c7<\/em>\u00a02-mapping procedures, via grid-search and Monte Carlo methods, to enhance and assess fitting accuracy. The presentation features allow users to seamlessly traverse the large amount of results, and the RD Simulator feature can help design future experiments as well as serve as a teaching tool for those unfamiliar with RD phenomena. Based on these innovative features, we expect that GUARDD will fill a well-defined gap in service of the RD NMR community.<\/p>\n","protected":false},"excerpt":{"rendered":"

Quick Links: MESMER – Minimal Ensemble Solutions to Multiple Experimental Data GUARDD –\u00a0Graphical User-friendly Analysis of Relaxation Dispersion Data PyMOL OSU Site License Info MESMER   Many (if not most) biological processes require structural, configurational, or compositional flexibility. DNA binding<\/p>\n","protected":false},"author":3,"featured_media":0,"parent":0,"menu_order":3,"comment_status":"closed","ping_status":"closed","template":"","meta":{"jetpack_post_was_ever_published":false,"footnotes":""},"class_list":["post-22","page","type-page","status-publish","hentry"],"jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/P7sxod-m","jetpack-related-posts":[{"id":16,"url":"https:\/\/research.cbc.osu.edu\/foster.281\/publications\/","url_meta":{"origin":22,"position":0},"title":"Publications","author":"Eric Danhart","date":"August 8, 2013","format":false,"excerpt":"Selected Publications Ma X, Baktina M, Shulgina I, Cantara WA, Nagy ABK, Goto Y, Suga H, Foster MP, Musier-Forsyth K. Structural basis of tRNAPro acceptor stem recognition by a bacterial trans-editing domain. Nucleic Acids Res. 2023 May 8; 51(8):3988-3999. doi: 10.1093\/nar\/gkad192. Li W, Norris AS, Lichtenthal K, Kelly S, Ihms\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"rid_logo","src":"https:\/\/i0.wp.com\/research.cbc.osu.edu\/foster.281\/wp-content\/uploads\/2013\/08\/rid_logo.gif?ssl=1&resize=350%2C200","width":350,"height":200},"classes":[]},{"id":693,"url":"https:\/\/research.cbc.osu.edu\/foster.281\/links\/literature-presentations\/","url_meta":{"origin":22,"position":1},"title":"Literature Presentations","author":"Mark Foster","date":"February 5, 2016","format":false,"excerpt":"Literature Presentations in the Foster Lab Objectives Improve our breadth of knowledge of research in areas related to ours Increase the breadth of our understanding of problems, techniques and concepts related to our research Learn to read research literature critically, and to identify important knowledge or methodological gaps Practice our\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":991,"url":"https:\/\/research.cbc.osu.edu\/foster.281\/laboratory-notebooks\/","url_meta":{"origin":22,"position":2},"title":"Laboratory Notebooks","author":"Mark Foster","date":"May 7, 2016","format":false,"excerpt":"The laboratory notebook is the record you keep of the method and the results of your experiments. Your lab notebook should be clear and thorough so that anyone with some knowledge in science (including yourself) is able to interpret your notes and reproduce your results. Your lab notebook should be\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":1134,"url":"https:\/\/research.cbc.osu.edu\/foster.281\/departure-checklist\/","url_meta":{"origin":22,"position":3},"title":"Departure Checklist","author":"Mark Foster","date":"July 11, 2016","format":false,"excerpt":"Preparing to move on? Be sure to: Finish experiments and writing manuscripts -- this is VERY difficult to do after leaving the lab Provide soft and hard-bound copies of thesis to PI (if appropriate) Schedule meeting with PI and\/or lab manager Dispose of useless reagents and clean up lab area\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":1698,"url":"https:\/\/research.cbc.osu.edu\/foster.281\/foster-group-guide\/","url_meta":{"origin":22,"position":4},"title":"Foster Group Guide","author":"Mark Foster","date":"March 26, 2021","format":false,"excerpt":"Foster Group Guide https:\/\/research.cbc.osu.edu\/foster.281\/foster-group-guide\/ Expectations A Ph.D. scientist is expected to be the world expert in the area of his\/her research. Consequently, a graduate education must produce a scientist capable of (1) thinking independently, (2) identifying a research problem (i.e., a testable hypothesis), (3) devising the means with which to\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":1869,"url":"https:\/\/research.cbc.osu.edu\/foster.281\/foster-group-guide-2\/","url_meta":{"origin":22,"position":5},"title":"Foster Group Guide","author":"Mark Foster","date":"April 18, 2023","format":false,"excerpt":"Foster Group Guide https:\/\/research.cbc.osu.edu\/foster.281\/foster-group-guide\/ Expectations A Ph.D. scientist is expected to be the world expert in the area of his\/her research. Consequently, a graduate education must produce a scientist capable of (1) thinking independently, (2) identifying a research problem (i.e., a testable hypothesis), (3) devising the means with which to\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]}],"_links":{"self":[{"href":"https:\/\/research.cbc.osu.edu\/foster.281\/wp-json\/wp\/v2\/pages\/22","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/research.cbc.osu.edu\/foster.281\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/research.cbc.osu.edu\/foster.281\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/research.cbc.osu.edu\/foster.281\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/research.cbc.osu.edu\/foster.281\/wp-json\/wp\/v2\/comments?post=22"}],"version-history":[{"count":15,"href":"https:\/\/research.cbc.osu.edu\/foster.281\/wp-json\/wp\/v2\/pages\/22\/revisions"}],"predecessor-version":[{"id":1344,"href":"https:\/\/research.cbc.osu.edu\/foster.281\/wp-json\/wp\/v2\/pages\/22\/revisions\/1344"}],"wp:attachment":[{"href":"https:\/\/research.cbc.osu.edu\/foster.281\/wp-json\/wp\/v2\/media?parent=22"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}