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Computational protein design: The proteus software and selected applications

dc.contributor.authorSimonson, Thomasen
dc.contributor.authorGaillard, Thomasen
dc.contributor.authorMignon, Daviden
dc.contributor.authorSchmidt, am Buschen
dc.contributor.authorLopes, Anneen
dc.contributor.authorAmara, Najetteen
dc.contributor.authorPolydorides, Savvasen
dc.contributor.authorSedano, Audreyen
dc.contributor.authorDruart, Karenen
dc.contributor.authorArchontis, Georgios Z.en
dc.creatorSimonson, Thomasen
dc.creatorGaillard, Thomasen
dc.creatorMignon, Daviden
dc.creatorSchmidt, am Buschen
dc.creatorLopes, Anneen
dc.creatorAmara, Najetteen
dc.creatorPolydorides, Savvasen
dc.creatorSedano, Audreyen
dc.creatorDruart, Karenen
dc.creatorArchontis, Georgios Z.en
dc.date.accessioned2019-12-02T15:32:38Z
dc.date.available2019-12-02T15:32:38Z
dc.date.issued2013
dc.identifier.urihttp://gnosis.library.ucy.ac.cy/handle/7/59050
dc.source.urihttps://nls.ldls.org.uk/welcome.html?ark:/81055/vdc_100024731727.0x000042
dc.subjectData processingen
dc.subjectChemistryen
dc.titleComputational protein design: The proteus software and selected applicationsen
dc.typeinfo:eu-repo/semantics/article
dc.description.startingpage1
dc.description.endingpageonline
dc.author.facultyΣχολή Θετικών και Εφαρμοσμένων Επιστημών / Faculty of Pure and Applied Sciences
dc.author.departmentΤμήμα Φυσικής / Department of Physics
dc.type.uhtypeArticleen
dc.description.notes<p>ID: 1032en
dc.description.notesIn: Journal of computational chemistry, Vol. 34, no. 28 ( 2013), p.2472-2484.en
dc.description.notesSummary: Abstract We describe an automated procedure for protein design, implemented in a flexible software package, called Proteus. System setup and calculation of an energy matrix are done with the XPLOR modeling program and its sophisticated command language, supporting several force fields and solvent models. A second program provides algorithms to search sequence space. It allows a decomposition of the system into groups, which can be combined in different ways in the energy function, for both positive and negative design. The whole procedure can be controlled by editing 2–4 scripts. Two applications consider the tyrosyl‐tRNA synthetase enzyme and its successful redesign to bind both O‐methyl‐tyrosine and D‐tyrosine. For the latter, we present Monte Carlo simulations where the D‐tyrosine concentration is gradually increased, displacing L‐tyrosine from the binding pocket and yielding the binding free energy difference, in good agreement with experiment. Complete redesign of the Crk SH3 domain is presented. The top 10000 sequences are all assigned to the correct fold by the SUPERFAMILY library of Hidden Markov Models. Finally, we report the acid/base behavior of the SNase protein. Sidechain protonation is treated as a form of mutationen
dc.description.notesit is then straightforward to perform constant‐pH Monte Carlo simulations, which yield good agreement with experiment. Overall, the software can be used for a wide range of application, producing not only native‐like sequences but also thermodynamic properties with errors that appear comparable to other current software packages.Copyright © 2013 Wiley Periodicals, Inc.</p>en
dc.contributor.orcidArchontis, Georgios Z. [0000-0002-7750-8641]
dc.gnosis.orcid0000-0002-7750-8641


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