{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:44:50Z","timestamp":1740185090483,"version":"3.37.3"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2017,1,31]],"date-time":"2017-01-31T00:00:00Z","timestamp":1485820800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["GM079804"],"award-info":[{"award-number":["GM079804"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Transmembrane beta-barrel proteins (TMBs) serve a multitude of essential cellular functions in Gram-negative bacteria, mitochondria and chloroplasts. Transfer free energies (TFEs) of residues in the transmembrane (TM) region provides fundamental quantifications of thermodynamic stabilities of TMBs, which are important for the folding and the membrane insertion processes, and may help in understanding the structure\u2013function relationship. However, experimental measurement of TFEs of TMBs is challenging. Although a recent computational method can be used to calculate TFEs, the results of which are in excellent agreement with experimentally measured values, this method does not scale up, and is limited to small TMBs.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We have developed an approximation method that calculates TFEs of TM residues in TMBs accurately, with which depth-dependent transfer free energy profiles can be derived. Our results are in excellent agreement with experimental measurements. This method is efficient and applicable to all bacterial TMBs regardless of the size of the protein.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>An online webserver is available at http:\/\/tanto.bioe.uic.edu\/tmb-tfe.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx053","type":"journal-article","created":{"date-parts":[[2017,1,30]],"date-time":"2017-01-30T13:28:22Z","timestamp":1485782902000},"page":"1664-1671","source":"Crossref","is-referenced-by-count":3,"title":["Efficient computation of transfer free energies of amino acids in beta-barrel membrane proteins"],"prefix":"10.1093","volume":"33","author":[{"given":"Wei","family":"Tian","sequence":"first","affiliation":[{"name":"Richard and Loan Hill Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Meishan","family":"Lin","sequence":"additional","affiliation":[{"name":"Richard and Loan Hill Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hammad","family":"Naveed","sequence":"additional","affiliation":[{"name":"Toyota Technological Institute at Chicago, Chicago, IL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jie","family":"Liang","sequence":"additional","affiliation":[{"name":"Richard and Loan Hill Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,1,31]]},"reference":[{"key":"2023020205303868200_btx053-B1","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1002\/prot.20456","article-title":"Empirical lipid propensities of amino acid residues in multispan alpha helical membrane proteins","volume":"59","author":"Adamian","year":"2005","journal-title":"Proteins"},{"key":"2023020205303868200_btx053-B2","doi-asserted-by":"crossref","first-page":"10244","DOI":"10.1021\/bi301398j","article-title":"Antibiotic uptake through membrane channels: role of Providencia stuartii omppst1 porin in carbapenem resistance","volume":"51","author":"Bajaj","year":"2012","journal-title":"Biochemistry"},{"key":"2023020205303868200_btx053-B3","doi-asserted-by":"crossref","first-page":"e62277","DOI":"10.1371\/journal.pone.0062277","article-title":"TOM40 mediates mitochondrial dysfunction induced by \u03b1-synuclein accumulation in Parkinson\u2019s disease","volume":"8","author":"Bender","year":"2013","journal-title":"PLoS ONE"},{"key":"2023020205303868200_btx053-B4","doi-asserted-by":"crossref","first-page":"10149","DOI":"10.1021\/ac4014836","article-title":"Sensing single mixed-monolayer protected gold nanoparticles by the \u03b1-hemolysin nanopore","volume":"85","author":"Campos","year":"2013","journal-title":"Anal. 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