{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T20:00:35Z","timestamp":1773345635787,"version":"3.50.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Circular dichroism (CD) is widely used in studies of protein folding. The CD spectrum of a protein can be estimated from its structure alone, using the well-established matrix method. In the last decade, a related spectroscopy, linear dichroism (LD), has been increasingly applied to study the orientation of proteins in solution. However, matrix method calculations of LD spectra have not been presented before. DichroCalc makes both CD and LD calculations available in an easy-to-use fashion.<\/jats:p><jats:p>Results: DichroCalc can be used without registration and calculates CD and LD spectra using a variety of matrix method parameters. PDB files can be uploaded as input or retrieved via their PDB code and a Perl-based parser is offered for easy handling of PDB files.<\/jats:p><jats:p>Availability: \u00a0http:\/\/comp.chem.nottingham.ac.uk\/dichrocalc and http:\/\/comp.chem.nottingham.ac.uk\/parsepdb<\/jats:p><jats:p>Contact: \u00a0jonathan.hirst@nottingham.ac.uk<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp016","type":"journal-article","created":{"date-parts":[[2009,1,8]],"date-time":"2009-01-08T01:24:23Z","timestamp":1231377863000},"page":"539-540","source":"Crossref","is-referenced-by-count":115,"title":["DichroCalc\u2014circular and linear dichroism online"],"prefix":"10.1093","volume":"25","author":[{"given":"Benjamin M.","family":"Bulheller","sequence":"first","affiliation":[{"name":"1 School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK"}]},{"given":"Jonathan D.","family":"Hirst","sequence":"additional","affiliation":[{"name":"1 School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK"}]}],"member":"286","published-online":{"date-parts":[[2009,1,7]]},"reference":[{"key":"2023013110114881300_B1","doi-asserted-by":"crossref","first-page":"11363","DOI":"10.1021\/jp0122833","article-title":"Ligand substituents of ruthenium dipyridophenazine complexes sensitively determine orientation in liposome membrane","volume":"105","author":"Ardhammar","year":"2001","journal-title":"J. Phys. Chem. B"},{"key":"2023013110114881300_B2","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1021\/j100721a038","article-title":"The rotatory properties of molecules containing two peptide groups","volume":"73","author":"Bayley","year":"1969","journal-title":"J. Phys. Chem."},{"key":"2023013110114881300_B3","doi-asserted-by":"crossref","first-page":"9636","DOI":"10.1021\/ja990627l","article-title":"Theoretical studies toward quantitative protein circular dichroism calculations","volume":"121","author":"Besley","year":"1999","journal-title":"J. Am. Chem. Soc."},{"key":"2023013110114881300_B4","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1002\/jcc.540040211","article-title":"CHARMM \u2013 a program for macromolecular energy, minimization, and dynamics calculations","volume":"4","author":"Brooks","year":"1983","journal-title":"J. Comput. Chem."},{"key":"2023013110114881300_B5","doi-asserted-by":"crossref","first-page":"2020","DOI":"10.1039\/b615870f","article-title":"Circular and linear dichroism of proteins","volume":"9","author":"Bulheller","year":"2007","journal-title":"Phys. Chem. Chem. Phys."},{"key":"2023013110114881300_B6","doi-asserted-by":"crossref","first-page":"1866","DOI":"10.1021\/jp077462k","article-title":"Charge-transfer transitions in the vacuum-ultraviolet of protein circular dichroism spectra","volume":"112","author":"Bulheller","year":"2008","journal-title":"J. Phys. Chem. B"},{"key":"2023013110114881300_B7","doi-asserted-by":"crossref","first-page":"12414","DOI":"10.1021\/ja0644125","article-title":"Charge-transfer transitions in protein circular dichroism calculations","volume":"128","author":"Oakley","year":"2006","journal-title":"J. Am. Chem. Soc."},{"key":"2023013110114881300_B8","doi-asserted-by":"crossref","DOI":"10.1093\/oso\/9780198558972.001.0001","volume-title":"Circular Dichroism & Linear Dichroism.","author":"Rodger","year":"1997"},{"key":"2023013110114881300_B9","doi-asserted-by":"crossref","first-page":"4051","DOI":"10.1039\/B205080N","article-title":"Flow oriented linear dichroism to probe protein orientation in membrane environments","volume":"4","author":"Rodger","year":"2002","journal-title":"Phys. Chem. Chem. Phys."},{"key":"2023013110114881300_B10","doi-asserted-by":"crossref","first-page":"11191","DOI":"10.1021\/jp036081d","article-title":"Ab initio study of aromatic side chains of amino acids in gas phase and solution","volume":"107","author":"Rogers","year":"2003","journal-title":"J. Phys. Chem. A"},{"key":"2023013110114881300_B11","doi-asserted-by":"crossref","first-page":"1611","DOI":"10.1101\/gr.361602","article-title":"The BioPerl toolkit: Perl modules for the life sciences","volume":"12","author":"Stajich","year":"2002","journal-title":"Genome Res."},{"key":"2023013110114881300_B12","doi-asserted-by":"crossref","first-page":"W668","DOI":"10.1093\/nar\/gkh371","article-title":"Dichroweb, an online server for protein secondary structure analyses from circular dichroism spectroscopic data; http:\/\/www.cryst.bbk.ac.uk\/cdweb","volume":"32","author":"Whitmore","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023013110114881300_B13","doi-asserted-by":"crossref","first-page":"4927","DOI":"10.1063\/1.1840658","article-title":"Optical rotation of oriented helices. 3. Calculation of rotatory dispersion and circular dichroism of \u03b1- and 310-helix","volume":"46","author":"Woody","year":"1967","journal-title":"J. Chem. Phys."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/4\/539\/48985126\/bioinformatics_25_4_539.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/4\/539\/48985126\/bioinformatics_25_4_539.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,3,8]],"date-time":"2024-03-08T20:45:44Z","timestamp":1709930744000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/4\/539\/251270"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,1,7]]},"references-count":13,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2009,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp016","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,2,15]]},"published":{"date-parts":[[2009,1,7]]}}}