<> <http://www.w3.org/2000/01/rdf-schema#comment> "The repository administrator has not yet configured an RDF license."^^<http://www.w3.org/2001/XMLSchema#string> .
<> <http://xmlns.com/foaf/0.1/primaryTopic> <https://discovery.ucl.ac.uk/id/eprint/142401> .
<https://discovery.ucl.ac.uk/id/eprint/142401> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.org/ontology/bibo/AcademicArticle> .
<https://discovery.ucl.ac.uk/id/eprint/142401> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.org/ontology/bibo/Article> .
<https://discovery.ucl.ac.uk/id/eprint/142401> <http://purl.org/dc/terms/title> "Predicting Transmembrane Helix Packing Arrangements using Residue Contacts and a Force-Directed Algorithm"^^<http://www.w3.org/2001/XMLSchema#string> .
<https://discovery.ucl.ac.uk/id/eprint/142401> <http://purl.org/ontology/bibo/abstract> "Alpha-helical transmembrane proteins constitute roughly 30% of a typical genome and are involved in a wide variety of important biological processes including cell signalling, transport of membrane-impermeable molecules and cell recognition. Despite significant efforts to predict transmembrane protein topology, comparatively little attention has been directed toward developing a method to pack the helices together. Here, we present a novel approach to predict lipid exposure, residue contacts, helix-helix interactions and finally the optimal helical packing arrangement of transmembrane proteins. Using molecular dynamics data, we have trained and cross-validated a support vector machine (SVM) classifier to predict per residue lipid exposure with 69% accuracy. This information is combined with additional features to train a second SVM to predict residue contacts which are then used to determine helix-helix interaction with up to 65% accuracy under stringent cross-validation on a non-redundant test set. Our method is also able to discriminate native from decoy helical packing arrangements with up to 70% accuracy. Finally, we employ a force-directed algorithm to construct the optimal helical packing arrangement which demonstrates success for proteins containing up to 13 transmembrane helices. This software is freely available as source code from http://bioinf.cs.ucl.ac.uk/memsat/mempack/."^^<http://www.w3.org/2001/XMLSchema#string> .
<https://discovery.ucl.ac.uk/id/eprint/142401> <http://purl.org/dc/terms/date> "2010-03-19" .
<https://discovery.ucl.ac.uk/id/document/45880> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.org/ontology/bibo/Document> .
<https://discovery.ucl.ac.uk/id/eprint/142401> <http://purl.org/ontology/bibo/volume> "6" .
<https://discovery.ucl.ac.uk/id/eprint/142401> <http://purl.org/ontology/bibo/issue> "3" .
<https://discovery.ucl.ac.uk/id/org/ext-75ea6aaed5eb22783511e404c3474352> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://xmlns.com/foaf/0.1/Organization> .
<https://discovery.ucl.ac.uk/id/org/ext-75ea6aaed5eb22783511e404c3474352> <http://xmlns.com/foaf/0.1/name> "PUBLIC LIBRARY SCIENCE"^^<http://www.w3.org/2001/XMLSchema#string> .
<https://discovery.ucl.ac.uk/id/eprint/142401> <http://purl.org/dc/terms/publisher> <https://discovery.ucl.ac.uk/id/org/ext-75ea6aaed5eb22783511e404c3474352> .
<https://discovery.ucl.ac.uk/id/publication/ext-1553734X> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.org/ontology/bibo/Collection> .
<https://discovery.ucl.ac.uk/id/publication/ext-1553734X> <http://xmlns.com/foaf/0.1/name> "PLoS Computational Biology"^^<http://www.w3.org/2001/XMLSchema#string> .
<https://discovery.ucl.ac.uk/id/eprint/142401> <http://purl.org/dc/terms/isPartOf> <https://discovery.ucl.ac.uk/id/publication/ext-1553734X> .
<https://discovery.ucl.ac.uk/id/publication/ext-1553734X> <http://www.w3.org/2002/07/owl#sameAs> <urn:issn:1553734X> .
<https://discovery.ucl.ac.uk/id/publication/ext-1553734X> <http://purl.org/ontology/bibo/issn> "1553734X" .
<https://discovery.ucl.ac.uk/id/eprint/142401> <http://purl.org/ontology/bibo/status> <http://purl.org/ontology/bibo/status/published> .
<https://discovery.ucl.ac.uk/id/eprint/142401> <http://purl.org/dc/terms/creator> <https://discovery.ucl.ac.uk/id/person/ext-5e15a775cfc7fd7a4e92b8c0a7772c1c> .
<https://discovery.ucl.ac.uk/id/eprint/142401> <http://purl.org/ontology/bibo/authorList> <https://discovery.ucl.ac.uk/id/eprint/142401#authors> .
<https://discovery.ucl.ac.uk/id/eprint/142401#authors> <http://www.w3.org/1999/02/22-rdf-syntax-ns#_1> <https://discovery.ucl.ac.uk/id/person/ext-5e15a775cfc7fd7a4e92b8c0a7772c1c> .
<https://discovery.ucl.ac.uk/id/eprint/142401> <http://purl.org/dc/terms/creator> <https://discovery.ucl.ac.uk/id/person/ext-7e12efd25e0c4d982ffc0742217c7fe0> .
<https://discovery.ucl.ac.uk/id/eprint/142401> <http://purl.org/ontology/bibo/authorList> <https://discovery.ucl.ac.uk/id/eprint/142401#authors> .
<https://discovery.ucl.ac.uk/id/eprint/142401#authors> <http://www.w3.org/1999/02/22-rdf-syntax-ns#_2> <https://discovery.ucl.ac.uk/id/person/ext-7e12efd25e0c4d982ffc0742217c7fe0> .
<https://discovery.ucl.ac.uk/id/person/ext-7e12efd25e0c4d982ffc0742217c7fe0> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://xmlns.com/foaf/0.1/Person> .
<https://discovery.ucl.ac.uk/id/person/ext-7e12efd25e0c4d982ffc0742217c7fe0> <http://xmlns.com/foaf/0.1/givenName> "DT"^^<http://www.w3.org/2001/XMLSchema#string> .
<https://discovery.ucl.ac.uk/id/person/ext-7e12efd25e0c4d982ffc0742217c7fe0> <http://xmlns.com/foaf/0.1/familyName> "Jones"^^<http://www.w3.org/2001/XMLSchema#string> .
<https://discovery.ucl.ac.uk/id/person/ext-7e12efd25e0c4d982ffc0742217c7fe0> <http://xmlns.com/foaf/0.1/name> "DT Jones"^^<http://www.w3.org/2001/XMLSchema#string> .
<https://discovery.ucl.ac.uk/id/person/ext-5e15a775cfc7fd7a4e92b8c0a7772c1c> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://xmlns.com/foaf/0.1/Person> .
<https://discovery.ucl.ac.uk/id/person/ext-5e15a775cfc7fd7a4e92b8c0a7772c1c> <http://xmlns.com/foaf/0.1/givenName> "T"^^<http://www.w3.org/2001/XMLSchema#string> .
<https://discovery.ucl.ac.uk/id/person/ext-5e15a775cfc7fd7a4e92b8c0a7772c1c> <http://xmlns.com/foaf/0.1/familyName> "Nugent"^^<http://www.w3.org/2001/XMLSchema#string> .
<https://discovery.ucl.ac.uk/id/person/ext-5e15a775cfc7fd7a4e92b8c0a7772c1c> <http://xmlns.com/foaf/0.1/name> "T Nugent"^^<http://www.w3.org/2001/XMLSchema#string> .
<https://discovery.ucl.ac.uk/id/eprint/142401> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://eprints.org/ontology/EPrint> .
<https://discovery.ucl.ac.uk/id/eprint/142401> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://eprints.org/ontology/ArticleEPrint> .
<https://discovery.ucl.ac.uk/id/eprint/142401> <http://purl.org/dc/terms/isPartOf> <https://discovery.ucl.ac.uk/id/repository> .
<https://discovery.ucl.ac.uk/id/eprint/142401> <http://eprints.org/ontology/hasDocument> <https://discovery.ucl.ac.uk/id/document/45880> .
<https://discovery.ucl.ac.uk/id/document/45880> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://eprints.org/ontology/Document> .
<https://discovery.ucl.ac.uk/id/document/45880> <http://www.w3.org/2000/01/rdf-schema#label> "Predicting Transmembrane Helix Packing Arrangements using Residue Contacts and a Force-Directed Algorithm (PDF)"^^<http://www.w3.org/2001/XMLSchema#string> .
<https://discovery.ucl.ac.uk/id/document/45880> <http://eprints.org/relation/hasVolatileVersion> <https://discovery.ucl.ac.uk/id/document/84701> .
<https://discovery.ucl.ac.uk/id/document/45880> <http://eprints.org/relation/haspreviewThumbnailVersion> <https://discovery.ucl.ac.uk/id/document/84701> .
<https://discovery.ucl.ac.uk/id/document/45880> <http://eprints.org/relation/hasVersion> <https://discovery.ucl.ac.uk/id/document/84701> .
<https://discovery.ucl.ac.uk/id/document/45880> <http://eprints.org/ontology/hasFile> <https://discovery.ucl.ac.uk/id/eprint/142401/1/142401.pdf> .
<https://discovery.ucl.ac.uk/id/document/45880> <http://purl.org/dc/terms/hasPart> <https://discovery.ucl.ac.uk/id/eprint/142401/1/142401.pdf> .
<https://discovery.ucl.ac.uk/id/eprint/142401/1/142401.pdf> <http://www.w3.org/2000/01/rdf-schema#label> "142401.pdf"^^<http://www.w3.org/2001/XMLSchema#string> .
<https://discovery.ucl.ac.uk/id/eprint/142401> <http://eprints.org/ontology/hasDocument> <https://discovery.ucl.ac.uk/id/document/84701> .
<https://discovery.ucl.ac.uk/id/document/84701> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://eprints.org/ontology/Document> .
<https://discovery.ucl.ac.uk/id/document/84701> <http://www.w3.org/2000/01/rdf-schema#label> "Predicting Transmembrane Helix Packing Arrangements using Residue Contacts and a Force-Directed Algorithm (Image (PNG))"^^<http://www.w3.org/2001/XMLSchema#string> .
<https://discovery.ucl.ac.uk/id/document/84701> <http://eprints.org/relation/isVolatileVersionOf> <https://discovery.ucl.ac.uk/id/document/45880> .
<https://discovery.ucl.ac.uk/id/document/84701> <http://eprints.org/relation/ispreviewThumbnailVersionOf> <https://discovery.ucl.ac.uk/id/document/45880> .
<https://discovery.ucl.ac.uk/id/document/84701> <http://eprints.org/relation/isVersionOf> <https://discovery.ucl.ac.uk/id/document/45880> .
<https://discovery.ucl.ac.uk/id/document/84701> <http://eprints.org/ontology/hasFile> <https://discovery.ucl.ac.uk/id/eprint/142401/2/preview.png> .
<https://discovery.ucl.ac.uk/id/document/84701> <http://purl.org/dc/terms/hasPart> <https://discovery.ucl.ac.uk/id/eprint/142401/2/preview.png> .
<https://discovery.ucl.ac.uk/id/eprint/142401/2/preview.png> <http://www.w3.org/2000/01/rdf-schema#label> "preview.png"^^<http://www.w3.org/2001/XMLSchema#string> .
<https://discovery.ucl.ac.uk/id/eprint/142401> <http://eprints.org/ontology/hasDocument> <https://discovery.ucl.ac.uk/id/document/110000> .
<https://discovery.ucl.ac.uk/id/document/110000> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://eprints.org/ontology/Document> .
<https://discovery.ucl.ac.uk/id/document/110000> <http://www.w3.org/2000/01/rdf-schema#label> "Predicting Transmembrane Helix Packing Arrangements using Residue Contacts and a Force-Directed Algorithm (Other)"^^<http://www.w3.org/2001/XMLSchema#string> .
<https://discovery.ucl.ac.uk/id/document/110000> <http://eprints.org/relation/isVersionOf> <https://discovery.ucl.ac.uk/id/document/45880> .
<https://discovery.ucl.ac.uk/id/document/110000> <http://eprints.org/relation/isVolatileVersionOf> <https://discovery.ucl.ac.uk/id/document/45880> .
<https://discovery.ucl.ac.uk/id/document/110000> <http://eprints.org/relation/isIndexCodesVersionOf> <https://discovery.ucl.ac.uk/id/document/45880> .
<https://discovery.ucl.ac.uk/id/document/110000> <http://eprints.org/ontology/hasFile> <https://discovery.ucl.ac.uk/id/eprint/142401/3/indexcodes.txt> .
<https://discovery.ucl.ac.uk/id/document/110000> <http://purl.org/dc/terms/hasPart> <https://discovery.ucl.ac.uk/id/eprint/142401/3/indexcodes.txt> .
<https://discovery.ucl.ac.uk/id/eprint/142401/3/indexcodes.txt> <http://www.w3.org/2000/01/rdf-schema#label> "indexcodes.txt"^^<http://www.w3.org/2001/XMLSchema#string> .
<https://discovery.ucl.ac.uk/id/eprint/142401> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <https://discovery.ucl.ac.uk/id/eprint/142401/> .
<https://discovery.ucl.ac.uk/id/eprint/142401/> <http://purl.org/dc/elements/1.1/title> "HTML Summary of #142401 \n\nPredicting Transmembrane Helix Packing Arrangements using Residue Contacts and a Force-Directed Algorithm\n\n" .
<https://discovery.ucl.ac.uk/id/eprint/142401/> <http://purl.org/dc/elements/1.1/format> "text/html" .
<https://discovery.ucl.ac.uk/id/eprint/142401/> <http://xmlns.com/foaf/0.1/primaryTopic> <https://discovery.ucl.ac.uk/id/eprint/142401> .