{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2022,4,2]],"date-time":"2022-04-02T15:43:10Z","timestamp":1648914190950},"reference-count":17,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2014,6,27]],"date-time":"2014-06-27T00:00:00Z","timestamp":1403827200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Cheminform"],"published-print":{"date-parts":[[2014,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>A foundational library called MORT (Molecular Objects and Relevant Templates) for the development of new software packages and tools employed in computational biology and computer-aided drug design (CADD) is described here.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>MORT contains several advantages compared with the other libraries. Firstly, MORT written in C++ natively supports the paradigm of object-oriented design, and thus it can be understood and extended easily. Secondly, MORT employs the relational model to represent a molecule, and it is more convenient and flexible than the traditional hierarchical model employed by many other libraries. Thirdly, a lot of functions have been included in this library, and a molecule can be manipulated easily at different levels. For example, it can parse a variety of popular molecular formats (MOL\/SDF, MOL2, PDB\/ENT, SMILES\/SMARTS, etc.), create the topology and coordinate files for the simulations supported by AMBER, calculate the energy of a specific molecule based on the AMBER force fields, etc.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>We believe that MORT can be used as a foundational library for programmers to develop new programs and applications for computational biology and CADD. Source code of MORT is available at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/cadd.suda.edu.cn\/MORT\/index.htm\" ext-link-type=\"uri\">http:\/\/cadd.suda.edu.cn\/MORT\/index.htm<\/jats:ext-link>.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1758-2946-6-36","type":"journal-article","created":{"date-parts":[[2014,6,27]],"date-time":"2014-06-27T01:02:57Z","timestamp":1403830977000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["MORT: a powerful foundational library for computational biology and CADD"],"prefix":"10.1186","volume":"6","author":[{"given":"Qian","family":"Zhang","sequence":"first","affiliation":[]},{"given":"Wei","family":"Zhang","sequence":"additional","affiliation":[]},{"given":"Youyong","family":"Li","sequence":"additional","affiliation":[]},{"given":"Junmei","family":"Wang","sequence":"additional","affiliation":[]},{"given":"Jian","family":"Zhang","sequence":"additional","affiliation":[]},{"given":"Tingjun","family":"Hou","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2014,6,27]]},"reference":[{"issue":"9","key":"612_CR1","doi-asserted-by":"publisher","first-page":"1278","DOI":"10.1093\/bioinformatics\/bts139","volume":"28","author":"P Andrio","year":"2012","unstructured":"Andrio P, Fenollosa C, Cicin-Sain D, Orozco M, Gelp\u00ed JL: MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations. 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