{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,12]],"date-time":"2025-10-12T20:00:01Z","timestamp":1760299201229},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"24","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Modern biotechnical research is becoming increasingly reliant on computational structural modeling programs to develop novel solutions to scientific questions. Rosetta is one such protein modeling suite that has already demonstrated wide applicability to a number of diverse research projects. Unfortunately, Rosetta is largely a command-line-driven software package which restricts its use among non-computational researchers. Some graphical interfaces for Rosetta exist, but typically are not as sophisticated as commercial software. Here, we present InteractiveROSETTA, a graphical interface for the PyRosetta framework that presents easy-to-use controls for several of the most widely used Rosetta protocols alongside a sophisticated selection system utilizing PyMOL as a visualizer. InteractiveROSETTA is also capable of interacting with remote Rosetta servers, facilitating sophisticated protocols that are not accessible in PyRosetta or which require greater computational resources.<\/jats:p>\n               <jats:p>Availability and implementation: InteractiveROSETTA is freely available at https:\/\/github.com\/schenc3\/InteractiveROSETTA\/releases and relies upon a separate download of PyRosetta which is available at http:\/\/www.pyrosetta.org after obtaining a license (free for academic use).<\/jats:p>\n               <jats:p>Contact: \u00a0bystrc@rpi.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv492","type":"journal-article","created":{"date-parts":[[2015,8,28]],"date-time":"2015-08-28T00:18:54Z","timestamp":1440721134000},"page":"4023-4025","source":"Crossref","is-referenced-by-count":18,"title":["InteractiveROSETTA: a graphical user interface for the PyRosetta protein modeling suite"],"prefix":"10.1093","volume":"31","author":[{"given":"Christian D.","family":"Schenkelberg","sequence":"first","affiliation":[{"name":"1 Department of Biological Sciences and"}]},{"given":"Christopher","family":"Bystroff","sequence":"additional","affiliation":[{"name":"1 Department of Biological Sciences and"},{"name":"2 Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY 12180, USA"}]}],"member":"286","published-online":{"date-parts":[[2015,8,26]]},"reference":[{"key":"2023051307185705100_btv492-B1","doi-asserted-by":"crossref","first-page":"e66856","DOI":"10.1371\/journal.pone.0066856","article-title":"The PyRosetta toolkit: a graphical user interface for the Rosetta software suite","volume":"8","author":"Adolf-Bryfogle","year":"2013","journal-title":"PLoS One"},{"key":"2023051307185705100_btv492-B2","doi-asserted-by":"crossref","first-page":"e21931","DOI":"10.1371\/journal.pone.0021931","article-title":"Real-time PyMOL visualization for Rosetta and PyRosetta","volume":"6","author":"Baugh","year":"2011","journal-title":"PLoS One"},{"key":"2023051307185705100_btv492-B3","doi-asserted-by":"crossref","first-page":"1068","DOI":"10.1016\/j.jmb.2008.05.042","article-title":"Conformer selection and induced fit in flexible backbone protein\u2013protein docking using computational and NMR ensembles","volume":"381","author":"Chaudhury","year":"2008","journal-title":"J. Mol. Biol."},{"key":"2023051307185705100_btv492-B4","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1093\/bioinformatics\/btq007","article-title":"PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta","volume":"26","author":"Chaudhury","year":"2010","journal-title":"Bioinformatics"},{"key":"2023051307185705100_btv492-B5","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1002\/prot.10529","article-title":"Automated prediction of CASP-5 structures using the Robetta server","volume":"53","author":"Chivian","year":"2003","journal-title":"Proteins"},{"key":"2023051307185705100_btv492-B6","doi-asserted-by":"crossref","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","article-title":"Biopython: freely available Python tools for computational molecular biology and bioinformatics","volume":"25","author":"Cock","year":"2009","journal-title":"Bioinformatics"},{"key":"2023051307185705100_btv492-B7","first-page":"82","article-title":"Pymol: An open-source molecular graphics tool","volume":"40","author":"DeLano","year":"2002","journal-title":"CCP4 Newsletter On Protein Crystallography"},{"key":"2023051307185705100_btv492-B8","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1186\/1471-2105-5-113","article-title":"MUSCLE: a multiple sequence alignment method with reduced time and space complexity","volume":"5","author":"Edgar","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"2023051307185705100_btv492-B9","doi-asserted-by":"crossref","first-page":"e20161","DOI":"10.1371\/journal.pone.0020161","article-title":"RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite","volume":"6","author":"Fleishman","year":"2011","journal-title":"PLoS One"},{"key":"2023051307185705100_btv492-B10","doi-asserted-by":"crossref","first-page":"2577","DOI":"10.1002\/bip.360221211","article-title":"Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features","volume":"22","author":"Kabsch","year":"1983","journal-title":"Biopolymers"},{"key":"2023051307185705100_btv492-B11","doi-asserted-by":"crossref","first-page":"18949","DOI":"10.1073\/pnas.1115898108","article-title":"Algorithm discovery by protein folding game players","volume":"108","author":"Khatib","year":"2011","journal-title":"Proc. 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A."},{"key":"2023051307185705100_btv492-B12","doi-asserted-by":"crossref","first-page":"1364","DOI":"10.1126\/science.1089427","article-title":"Design of a novel globular protein fold with atomic-level accuracy","volume":"302","author":"Kuhlman","year":"2003","journal-title":"Science"},{"key":"2023051307185705100_btv492-B13","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1016\/B978-0-12-381270-4.00019-6","article-title":"Rosetta3: an object-oriented software suite for the simulation and design of macromolecules","volume":"487","author":"Leaver-Fay","year":"2011","journal-title":"Methods Enzymol."},{"key":"2023051307185705100_btv492-B14","doi-asserted-by":"crossref","first-page":"e63906","DOI":"10.1371\/journal.pone.0063906","article-title":"Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE)","volume":"8","author":"Lyskov","year":"2013","journal-title":"PLoS One"},{"key":"2023051307185705100_btv492-B15","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1038\/nmeth0809-551","article-title":"Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling","volume":"6","author":"Mandell","year":"2009","journal-title":"Nat. Methods"},{"key":"2023051307185705100_btv492-B17","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1002\/prot.22540","article-title":"Structure prediction for CASP8 with all-atom refinement using Rosetta","volume":"77","author":"Raman","year":"2009","journal-title":"Proteins"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/24\/4023\/50307111\/bioinformatics_31_24_4023.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/24\/4023\/50307111\/bioinformatics_31_24_4023.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,13]],"date-time":"2023-05-13T07:20:49Z","timestamp":1683962449000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/24\/4023\/197368"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,8,26]]},"references-count":16,"journal-issue":{"issue":"24","published-print":{"date-parts":[[2015,12,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv492","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,12,15]]},"published":{"date-parts":[[2015,8,26]]}}}