{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,2]],"date-time":"2026-05-02T22:15:59Z","timestamp":1777760159606,"version":"3.51.4"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2020,4,28]],"date-time":"2020-04-28T00:00:00Z","timestamp":1588032000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/J019194"],"award-info":[{"award-number":["BB\/J019194"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/P024106"],"award-info":[{"award-number":["BB\/P024106"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>PDBMD2CD is a new web server capable of predicting circular dichroism (CD) spectra for multiple protein structures derived from molecular dynamics (MD) simulations, enabling predictions from thousands of protein atomic coordinate files (e.g. MD trajectories) and generating spectra for each of these structures provided by the user. Using MD enables exploration of systems that cannot be monitored by direct experimentation. Validation of MD-derived data from these types of trajectories can be difficult via conventional structure-determining techniques such as crystallography or nuclear magnetic resonance spectroscopy. CD is an experimental technique that can provide protein structure information from such conditions. The website utilizes a much faster (minimum \u223c1000\u00d7) and more accurate approach for calculating CD spectra than its predecessor, PDB2CD (1). As well as improving on the speed and accuracy of current methods, new analysis tools are provided to cluster predictions or compare them against experimental CD spectra. By identifying a subset of the closest predicted CD spectra derived from PDBMD2CD to an experimental spectrum, the associated cluster of structures could be representative of those found under the conditions in which the MD studies were undertaken, thereby offering an analytical insight into the results.\u00a0PDBMD2CD is freely available at: https:\/\/pdbmd2cd.cryst.bbk.ac.uk.<\/jats:p>","DOI":"10.1093\/nar\/gkaa296","type":"journal-article","created":{"date-parts":[[2020,4,25]],"date-time":"2020-04-25T19:08:19Z","timestamp":1587841699000},"page":"W17-W24","source":"Crossref","is-referenced-by-count":82,"title":["PDBMD2CD: providing predicted protein circular dichroism spectra from multiple molecular dynamics-generated protein structures"],"prefix":"10.1093","volume":"48","author":[{"given":"Elliot D","family":"Drew","sequence":"first","affiliation":[{"name":"School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5483-6282","authenticated-orcid":false,"given":"Robert W","family":"Janes","sequence":"first","affiliation":[{"name":"School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,4,28]]},"reference":[{"key":"2020062614050909800_B1","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1093\/bioinformatics\/btw554","article-title":"PDB2CD: a web-based application for the generation of circular dichroism spectra from protein atomic coordinates","volume":"33","author":"Mavridis","year":"2017","journal-title":"Bioinformatics"},{"key":"2020062614050909800_B2","doi-asserted-by":"crossref","first-page":"3340","DOI":"10.1111\/febs.14869","article-title":"The GRASP domain in golgi reassembly and stacking proteins: differences and similarities between lower and higher Eukaryotes","volume":"286","author":"Mendes","year":"2019","journal-title":"FEBS J."},{"key":"2020062614050909800_B3","doi-asserted-by":"crossref","first-page":"1094","DOI":"10.1016\/j.str.2019.03.019","article-title":"Structural insights into bacteriophage GIL01 gp7 inhibition of host LexA repressor","volume":"27","author":"Caveney","year":"2019","journal-title":"Structure"},{"key":"2020062614050909800_B4","doi-asserted-by":"crossref","first-page":"1680","DOI":"10.1021\/acschemneuro.8b00065","article-title":"Amyloid-\u03b2 Peptide interactions with amphiphilic surfactants: electrostatic and hydrophobic effects","volume":"9","author":"Osterlund","year":"2018","journal-title":"ACS Chem. 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