TMRPres2D: high quality visual representation of transmembrane protein models

被引：116

作者：

Spyropoulos, IC ^{[1
]}

Liakopoulos, TD ^{[1
]}

Bagos, PG ^{[1
]}

Hamodrakas, SJ ^{[1
]}

机构：

[1] Univ Athens, Fac Biol, Dept Cell Biol & Biophys, Athens 15701, Greece

来源：

BIOINFORMATICS | 2004年 / 20卷 / 17期

关键词：

D O I：

10.1093/bioinformatics/bth358

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

The 'TransMembrane protein Re-Presentation in 2-Dimensions' (TMRPres2D) tool, automates the creation of uniform, two-dimensional, high analysis graphical images/models of alpha-helical or beta-barrel transmembrane proteins. Protein sequence data and structural information may be acquired from public protein knowledge bases, emanate from prediction algorithms, or even be defined by the user. Several important biological and physical sequence attributes can be embedded in the graphical representation.

引用

页码：3258 / 3260

页数：3

共 14 条

[1]

Andersen Claus A F, 2003, Methods Biochem Anal, V44, P341

[2]

Apweiler R, 2004, NUCLEIC ACIDS RES, V32, pD115, DOI [10.1093/nar/gkw1099, 10.1093/nar/gkh131]

[3] A Hidden Markov Model method, capable of predicting and discriminating β-barrel outer membrane proteins -: art. no. 29 [J].

Bagos, PG ;

Liakopoulos, TD ;

Spyropoulos, IC ;

Hamodrakas, SJ .

BMC BIOINFORMATICS, 2004, 5 (1)

[4] TEXtopo:: shaded membrane protein topology plots in LATEX2ε [J].

Beitz, E .

BIOINFORMATICS, 2000, 16 (11) :1050-1051

[5] The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 [J].

Boeckmann, B ;

Bairoch, A ;

Apweiler, R ;

Blatter, MC ;

Estreicher, A ;

Gasteiger, E ;

Martin, MJ ;

Michoud, K ;

O'Donovan, C ;

Phan, I ;

Pilbout, S ;

Schneider, M .

NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :365-370

[6] Schematic representation of residue-based protein context-dependent data: An application to transmembrane proteins [J].

Campagne, F ;

Weinstein, H .

JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 1999, 17 (3-4) :207-213

[7] Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes [J].

Krogh, A ;

Larsson, B ;

von Heijne, G ;

Sonnhammer, ELL .

JOURNAL OF MOLECULAR BIOLOGY, 2001, 305 (03) :567-580

[8] VHMPT: a graphical viewer and editor for helical membrane protein topologies [J].

Lin, WJ ;

Hwang, MJ .

BIOINFORMATICS, 1998, 14 (10) :866-868

[9] TOPS: an enhanced database of protein structural topology [J].

Michalopoulos, I ;

Torrance, GM ;

Gilbert, DR ;

Westhead, DR .

NUCLEIC ACIDS RESEARCH, 2004, 32 :D251-D254

[10] A novel method for predicting transmembrane segments in proteins based on a statistical analysis of the SwissProt database: the PRED-TMR algorithm [J].

Pasquier, C ;

Promponas, VJ ;

Palaios, GA ;

Hamodrakas, JS ;

Hamodrakas, SJ .

PROTEIN ENGINEERING, 1999, 12 (05) :381-385

← 1 2 →