DOI: 10.1016/s0022-2836(03)00182-7. Reliability Measures for Membrane Protein Topology Prediction Algorithms

Reliability Measures for Membrane Protein Topology Prediction Algorithms

10.1016/s0022-2836(03)00182-7

Crossref journal-article

Elsevier BV

Journal of Molecular Biology (78)

Authors 3

Karin Melén (first)
Anders Krogh (additional)
Gunnar von Heijne (additional)

References 26 Referenced 166

10.1006/jmbi.2000.4315 / J. Mol. Biol. / Predicting transmembrane protein topology with a hidden Markov model. Application to complete genomes by Krogh (2001)
10.1093/nar/28.1.235 / Nucl. Acids Res. / The Protein Data Bank by Berman (2000)
10.1006/jmbi.1998.2107 / J. Mol. Biol. / Principles governing amino acid composition of integral membrane proteins: application to topology prediction by Tusnady (1998)
10.1021/bi00176a037 / Biochemistry / A model recognition approach to the prediction of all-helical membrane protein structure and topology by Jones (1994)
10.1002/pro.5560050824 / Protein Sci. / Topology prediction for helical transmembrane proteins at 86% accuracy by Rost (1996)
10.1016/0022-2836(92)90934-C / J. Mol. Biol. / Membrane protein structure prediction—hydrophobicity analysis and the positive-inside rule by von Heijne (1992)
10.1093/bioinformatics/17.7.646 / Bioinformatics / Evaluations of methods for the predictive evaluation of membrane spanning regions by Möller (2001)
{'key': '10.1016/S0022-2836(03)00182-7_BIB8', 'first-page': '1', 'article-title': 'Transmembrane topology prediction methods: a re-assessment and improvement by a consensus method using a data-set of experimentally characterized transmembrane topologies', 'volume': '2', 'author': 'Ikeda', 'year': '2001', 'journal-title': 'In Silico Biol.'} / In Silico Biol. / Transmembrane topology prediction methods: a re-assessment and improvement by a consensus method using a data-set of experimentally characterized transmembrane topologies by Ikeda (2001)
10.1016/S0022-2836(05)80360-2 / J. Mol. Biol. / Basic local alignment search tool by Altschul (1990)
10.1093/bib/3.3.275 / Brief. Bioinformat. / High-quality protein knowledge resource: SWISS-PROT and TrEMBL by O'Donovan (2002)
10.1002/j.1460-2075.1986.tb04601.x / EMBO J. / The distribution of positively charged residues in bacterial inner membrane proteins correlates with the trans-membrane topology by von Heijne (1986)
10.1038/341456a0 / Nature / Control of topology and mode of assembly of a polytopic membrane protein by positively charged residues by von Heijne (1989)
10.1016/S0014-5793(02)03730-4 / FEBS Letters / Reliability of transmembrane predictions in whole-genome data by Käll (2002)
10.1110/ps.0226702 / Protein Sci. / Prediction of partial membrane protein topologies using a consensus approach by Nilsson (2002)
10.1126/science.277.5331.1453 / Science / The complete genome sequence of Escherichia coli K-12 by Blattner (1997)
{'key': '10.1016/S0022-2836(03)00182-7_BIB16', 'first-page': '1', 'article-title': 'The yeast genome directory', 'volume': 'suppl. 387', 'author': 'Goffeau', 'year': '1997', 'journal-title': 'Nature'} / Nature / The yeast genome directory by Goffeau (1997)
10.1093/nar/29.1.82 / Nucl. Acids Res. / WormBase: network access to the genome and biology of Caenorhabditis elegans by Stein (2001)
10.1126/science.282.5396.2028 / Science / Neurobiology of the Caenorhabditis elegans genome by Bargmann (1998)
10.1073/pnas.052018199 / Proc. Natl Acad. Sci. USA / Rapid topology mapping of Escherichia coli inner-membrane proteins by prediction and PhoA/GFP fusion analysis by Drew (2002)
10.1016/S0091-679X(08)61676-3 / Methods Cell. Biol. / Analysis of membrane protein topology using alkaline phosphatase and β-galactosidase gene fusions by Manoil (1991)
10.1074/jbc.M008608200 / J. Biol. Chem. / Membrane topology and function of Der3/Hrd1p as a ubiquitin-protein ligase (E3) involved in endoplasmic reticulum degradation by Deak (2001)
10.1074/jbc.272.29.18325 / J. Biol. Chem. / Mapping the ends of transmembrane segments in a polytopic membrane protein—scanning N-glycosylation mutagenesis of extracytosolic loops in the anion exchanger, Band 3 by Popov (1997)
10.1093/bioinformatics/17.9.849 / Bioinformatics / The HMMTOP transmembrane topology prediction server by Tusnady (2001)
10.1093/bioinformatics/16.12.1159 / Bioinformatics / A collection of well-characterised integral membrane proteins by Möller (2000)
10.1093/nar/22.22.4673 / Nucl. Acids Res. / CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice by Thompson (1994)
10.1002/pro.5560010313 / Protein Sci. / Selection of representative protein data sets by Hobohm (1992)

Dates

Type	When
Created	22 years, 5 months ago (March 14, 2003, 9:10 p.m.)
Deposited	5 years, 5 months ago (March 17, 2020, 9:48 p.m.)
Indexed	2 months, 1 week ago (June 26, 2025, 8:46 a.m.)
Issued	22 years, 6 months ago (March 1, 2003)
Published	22 years, 6 months ago (March 1, 2003)
Published Print	22 years, 6 months ago (March 1, 2003)

Funders 0

None

BibTeX

@article{Mel_n_2003, title={Reliability Measures for Membrane Protein Topology Prediction Algorithms}, volume={327}, ISSN={0022-2836}, url={http://dx.doi.org/10.1016/s0022-2836(03)00182-7}, DOI={10.1016/s0022-2836(03)00182-7}, number={3}, journal={Journal of Molecular Biology}, publisher={Elsevier BV}, author={Melén, Karin and Krogh, Anders and von Heijne, Gunnar}, year={2003}, month=mar, pages={735–744} }

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