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• W594178905 abstract "Analysis of the complete genomic sequences for several organisms indicates that 20-25% of all genes code for transmembrane proteins (Jones, 1998, Wallin and von Heijne, 1998), yet only a very small number of transmembrane 3D structures are known. Hence, it is of great importance to develop theoretical methods capable of predicting transmembrane protein structure and function based on protein sequence alone. To address this, we sought to devise a systematic and high throughput method for identifying homologous transmembrane proteins. Since protein structure is more evolutionarily conserved than amino acid sequence, we predicted that adding structural information to simple sequence alignment would improve homology detection of transmembrane proteins. In the present work, we describe development of a search method that combines sequence alignment with structural information. In our method the initial sequence alignment searches are performed using PSI-BLAST. Then profiles derived from the multiple sequence alignments are input into a neural network, developed in this work to predict which transmembrane residues are buried (core of the helix-bundle) or exposed (to the lipid environment). A maximum accuracy of 86% was achieved. Moreover, for almost half of the query set, the predicted residue orientation was more than 70% accurate. In the last step of the work presented here, the predicted helix locations, residue orientations and loop length scores are added to the PSI-BLAST E-value, to create a ‘combined’ classifier. A linear equation was built for calculating the 'combined’ classifier score. Our method was evaluated using two databases of proteins: Pfam and GPCRDB. The Pfam database was chosen, as transmembrane proteins in this database have been classified into various families. GPCRDB was employed as this database, though narrow, is well-studied and maintained. Before building the ‘combined’ classifier, PSI-BLAST sequence alignment was benchmarked using the Pfam database. We found that our 'combined’ classifier, as compared to a classifier based solely on PSI-BLAST, resulted in more true positives with less false positives when tested using GPCRDB and could differentiate between GPCRDB families. However, our ‘combined’ classifier did not improve homology detection when searching transmembrane proteins from the Pfam database. A comparison of our ‘combined’ classifier method with two other published methods suggested that profile-profile based searches could be more powerful than profile-sequence based searches, even after the addition of structural information as described here. In light of our study, we propose that combining structural information with profile-profile sequence alignment into a 'combined’ classifier could result in a search method superior to any existing ones for detecting homologous transmembrane proteins." @default.
• W594178905 created "2016-06-24" @default.
• W594178905 creator A5008479232 @default.
• W594178905 date "2013-02-28" @default.
• W594178905 modified "2023-09-26" @default.
• W594178905 title "Developing a Novel Method for Homology Detection of Transmembrane Proteins" @default.
• W594178905 cites W1490329454 @default.
• W594178905 cites W1508885706 @default.
• W594178905 cites W1526754730 @default.
• W594178905 cites W1533540035 @default.
• W594178905 cites W1537016059 @default.
• W594178905 cites W1588000118 @default.
• W594178905 cites W1590648220 @default.
• W594178905 cites W1969051510 @default.
• W594178905 cites W1970758461 @default.
• W594178905 cites W1970861588 @default.
• W594178905 cites W1971147414 @default.
• W594178905 cites W1971449260 @default.
• W594178905 cites W1971894639 @default.
• W594178905 cites W1971912858 @default.
• W594178905 cites W1972961211 @default.
• W594178905 cites W1975304761 @default.
• W594178905 cites W1982533969 @default.
• W594178905 cites W1987303875 @default.
• W594178905 cites W1990081741 @default.
• W594178905 cites W1992596028 @default.
• W594178905 cites W1994025789 @default.
• W594178905 cites W1996357466 @default.
• W594178905 cites W1996795941 @default.
• W594178905 cites W2001900040 @default.
• W594178905 cites W2003144438 @default.
• W594178905 cites W2005034462 @default.
• W594178905 cites W2007562782 @default.
• W594178905 cites W2008708467 @default.
• W594178905 cites W2009899161 @default.
• W594178905 cites W2010879612 @default.
• W594178905 cites W2011235285 @default.
• W594178905 cites W2012534599 @default.
• W594178905 cites W2012604750 @default.
• W594178905 cites W2015292449 @default.
• W594178905 cites W2020478092 @default.
• W594178905 cites W2022496255 @default.
• W594178905 cites W2022777594 @default.
• W594178905 cites W2026258231 @default.
• W594178905 cites W2027711565 @default.
• W594178905 cites W2029195137 @default.
• W594178905 cites W2029470130 @default.
• W594178905 cites W2033948133 @default.
• W594178905 cites W2036123216 @default.
• W594178905 cites W2039330662 @default.
• W594178905 cites W2040198144 @default.
• W594178905 cites W2040700161 @default.
• W594178905 cites W2042521088 @default.
• W594178905 cites W2046267877 @default.
• W594178905 cites W2047567262 @default.
• W594178905 cites W2049732818 @default.
• W594178905 cites W2050625197 @default.
• W594178905 cites W2055043387 @default.
• W594178905 cites W2055118532 @default.
• W594178905 cites W2055136196 @default.
• W594178905 cites W2055549091 @default.
• W594178905 cites W2057972192 @default.
• W594178905 cites W2058336694 @default.
• W594178905 cites W2062693912 @default.
• W594178905 cites W2065510140 @default.
• W594178905 cites W2067395459 @default.
• W594178905 cites W2073110681 @default.
• W594178905 cites W2074231493 @default.
• W594178905 cites W2074765093 @default.
• W594178905 cites W2075130091 @default.
• W594178905 cites W2075696595 @default.
• W594178905 cites W2076048958 @default.
• W594178905 cites W2077246792 @default.
• W594178905 cites W2078051636 @default.
• W594178905 cites W2080855949 @default.
• W594178905 cites W2081629966 @default.
• W594178905 cites W2082148481 @default.
• W594178905 cites W2082667898 @default.
• W594178905 cites W2085277871 @default.
• W594178905 cites W2087009455 @default.
• W594178905 cites W2087064593 @default.
• W594178905 cites W2088749445 @default.
• W594178905 cites W2089047063 @default.
• W594178905 cites W2089606003 @default.
• W594178905 cites W2093615982 @default.
• W594178905 cites W2097518371 @default.
• W594178905 cites W2097775366 @default.
• W594178905 cites W2099075703 @default.
• W594178905 cites W2099946731 @default.
• W594178905 cites W2101466114 @default.
• W594178905 cites W2102122585 @default.
• W594178905 cites W2103112501 @default.
• W594178905 cites W2104061813 @default.
• W594178905 cites W2106068169 @default.
• W594178905 cites W2107432340 @default.
• W594178905 cites W2108758729 @default.
• W594178905 cites W2109261827 @default.
• W594178905 cites W2110425545 @default.
• W594178905 cites W2110673210 @default.
• W594178905 cites W2111373249 @default.

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