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There is a need, therefore, to develop accurate and sensitive alignment protocols.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>BioShell threading software is a versatile tool for aligning protein structures, protein sequences or sequence profiles and query sequences to a template structures. The software is also capable of sub-optimal alignment generation. It can be executed as an application from the UNIX command line, or as a set of Java classes called from a script or a Java application. The implemented Monte Carlo search engine greatly facilitates the development and benchmarking of new alignment scoring schemes even when the functions exhibit non-deterministic polynomial-time complexity.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Numerical experiments indicate that the new threading application offers template detection abilities and provides much better alignments than other methods. The package along with documentation and examples is available at: <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/bioshell.pl\/threading3d\" ext-link-type=\"uri\">http:\/\/bioshell.pl\/threading3d<\/jats:ext-link>.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-15-22","type":"journal-article","created":{"date-parts":[[2014,1,20]],"date-time":"2014-01-20T18:02:28Z","timestamp":1390240948000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["BioShell-Threading: versatile Monte Carlo package for protein 3D threading"],"prefix":"10.1186","volume":"15","author":[{"given":"Pawel","family":"Gniewek","sequence":"first","affiliation":[]},{"given":"Andrzej","family":"Kolinski","sequence":"additional","affiliation":[]},{"given":"Andrzej","family":"Kloczkowski","sequence":"additional","affiliation":[]},{"given":"Dominik","family":"Gront","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2014,1,20]]},"reference":[{"key":"6816_CR1","doi-asserted-by":"publisher","first-page":"779","DOI":"10.1006\/jmbi.1993.1626","volume":"234","author":"A Sali","year":"1993","unstructured":"Sali A, Blundell TL: Comparative protein modelling by satisfaction of spatial restraints. 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