On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins.

Biophysical Journal
Lucy R ForrestBarry H Honig

Abstract

In this study, we investigate the extent to which techniques for homology modeling that were developed for water-soluble proteins are appropriate for membrane proteins as well. To this end we present an assessment of current strategies for homology modeling of membrane proteins and introduce a benchmark data set of homologous membrane protein structures, called HOMEP. First, we use HOMEP to reveal the relationship between sequence identity and structural similarity in membrane proteins. This analysis indicates that homology modeling is at least as applicable to membrane proteins as it is to water-soluble proteins and that acceptable models (with C alpha-RMSD values to the native of 2 A or less in the transmembrane regions) may be obtained for template sequence identities of 30% or higher if an accurate alignment of the sequences is used. Second, we show that secondary-structure prediction algorithms that were developed for water-soluble proteins perform approximately as well for membrane proteins. Third, we provide a comparison of a set of commonly used sequence alignment algorithms as applied to membrane proteins. We find that high-accuracy alignments of membrane protein sequences can be obtained using state-of-the-art profile...Continue Reading

References

Nov 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·S Henikoff, J G Henikoff
Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Aug 4, 1989·Science·D C ReesD Eisenberg
Dec 1, 1986·Proceedings of the National Academy of Sciences of the United States of America·B A WallaceD L Mielke
Jun 1, 1994·Nature Structural Biology·S C Li, C M Deber
Aug 1, 1994·Nature Structural Biology·S C Li, C M Deber
Oct 28, 1994·Journal of Molecular Biology·M CserzöB Maigret
Feb 21, 1994·FEBS Letters·D T JonesJ M Thornton
Dec 5, 1993·Journal of Molecular Biology·A Sali, T L Blundell
Nov 1, 1993·Protein Science : a Publication of the Protein Society·T P FloresJ M Thornton
Jan 1, 1993·Protein Science : a Publication of the Protein Society·D DonnellyT L Blundell
Apr 1, 1997·Protein Science : a Publication of the Protein Society·E WallinA Elofsson
Oct 5, 1997·Biopolymers·S E BlondelleE Pérez-Payá
Mar 27, 1998·FEBS Letters·D T Jones
May 6, 1998·Protein Science : a Publication of the Protein Society·E Wallin, G von Heijne
May 22, 1998·Molecular Membrane Biology·J S Lolkema, D J Slotboom
Jun 22, 1999·Nucleic Acids Research·J D ThompsonO Poch
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Mar 17, 2000·Science·J Drews
Aug 31, 2000·Journal of Molecular Biology·C NotredameJ Heringa
Mar 10, 2001·Journal of Molecular Biology·R P RiekR M Graham
Sep 12, 2001·Journal of Structural Biology·B Rost
Feb 9, 2002·Proteins·B Rost, V A Eyrich
Feb 9, 2002·Proteins·Arne Elofsson
Feb 16, 2002·Protein Science : a Publication of the Protein Society·Maria HedmanArne Elofsson
May 3, 2002·European Journal of Biochemistry·John D Clements, Rowena E Martin
Jun 5, 2002·FEBS Letters·Rita CasadioVito De Pinto
Aug 10, 2002·Science·Werner KühlbrandtJens Dietrich
Nov 21, 2002·Protein Science : a Publication of the Protein Society·Chien Peter ChenBurkhard Rost
Dec 4, 2002·Proceedings of the National Academy of Sciences of the United States of America·Haruo Ogawa, Chikashi Toyoshima
Jun 26, 2003·Nucleic Acids Research·Adam Zemla
Oct 28, 2003·Proteins·Ceslovas VenclovasJohn Moult
Jan 31, 2004·Bioinformatics·Yinon Shafrir, H Robert Guy
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar

❮ Previous
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Citations

Jul 16, 2008·Journal of Molecular Modeling·Minyong LiBinghe Wang
Nov 26, 2010·Journal of Molecular Modeling·Assaf GanothIsaiah T Arkin
Mar 8, 2012·Journal of Computer-aided Molecular Design·Andrew J Heim, Zhijun Li
Oct 28, 2009·Journal of Structural and Functional Genomics·Marco PuntaBurkhard Rost
May 4, 2011·Journal of Chemical Information and Modeling·Kuldeep K Roy, Anil K Saxena
Apr 26, 2012·Journal of Chemical Information and Modeling·Amit K GuptaAnil K Saxena
Apr 2, 2013·Journal of Chemical Information and Modeling·Daniele PalaMarco Mor
Oct 17, 2013·Journal of Chemical Information and Modeling·Tim Werner, W Bret Church
Jul 25, 2009·Journal of Medicinal Chemistry·Juan Carlos MobarecMarta Filizola
Feb 5, 2009·Proceedings of the National Academy of Sciences of the United States of America·P BarthD Baker
Mar 27, 2013·Proceedings of the National Academy of Sciences of the United States of America·Dana YaffeShimon Schuldiner
Dec 1, 2010·The Journal of Biological Chemistry·Sotiria TavoulariGary Rudnick
Mar 27, 2013·The Journal of General Physiology·Kethika KulleperumaRégis Pomès
Nov 14, 2012·The Journal of General Physiology·Antonella GradognaMichael Pusch
Jan 5, 2008·Bioinformatics·Walter PirovanoJaap Heringa
Oct 12, 2010·Bioinformatics·Sebastian KelmCharlotte M Deane
Oct 16, 2010·Bioinformatics·Arjun RayBjörn Wallner
Jun 21, 2011·Bioinformatics·Jamie R HillCharlotte M Deane
Nov 1, 2012·Bioinformatics·Jamie R Hill, Charlotte M Deane
May 17, 2013·Bioinformatics·Mireia OlivellaXavier Deupi
May 26, 2009·Nucleic Acids Research·Alexander RosePeter W Hildebrand
May 4, 2013·Nucleic Acids Research·Jean-Paul EbejerCharlotte M Deane
Dec 5, 2008·Protein Engineering, Design & Selection : PEDS·Vagmita Pabuwal, Zhijun Li
Jun 21, 2007·Annual Review of Biochemistry·Arne Elofsson, Gunnar von Heijne
May 2, 2012·BMC Bioinformatics·Jia-Ming ChangCedric Notredame
Sep 8, 2009·Theoretical Biology & Medical Modelling·Aina W RavnaGeorg Sager
Oct 29, 2010·BMC Research Notes·Mirna Abraham-NordlingErik Nordling
Aug 17, 2010·PLoS Computational Biology·Jana SelentGianni De Fabritiis
Mar 29, 2014·PLoS Computational Biology·Jianzhu MaJinbo Xu
May 24, 2014·PLoS Computational Biology·Kuang-Yui M ChenPatrick Barth
Nov 22, 2011·PloS One·Assaf GanothIsaiah T Arkin
Mar 8, 2013·PloS One·Marcus StammLucy R Forrest
Jan 26, 2007·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Claire L PadgettSarah C R Lummis
Apr 29, 2014·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Jérôme WaldispühlBonnie Berger
Jul 1, 2009·Cellular and Molecular Life Sciences : CMLS·Uwe Ludewig, Marek Dynowski

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