PDBTM: Protein Data Bank of transmembrane proteins after 8 years

被引：197

作者：

Kozma, Daniel ^{[1
]}

Simon, Istvan ^{[2
]}

Tusnady, Gabor E. ^{[1
]}

机构：

[1] MTA RCNS, Inst Enzymol, Lendulet Membrane Prot Bioinformat Res Grp, H-1518 Budapest, Hungary

[2] MTA RCNS, Inst Enzymol, Prot Struct Res Grp, H-1518 Budapest, Hungary

来源：

NUCLEIC ACIDS RESEARCH | 2013年 / 41卷 / D1期

基金：

匈牙利科学研究基金会;

关键词：

MEMBRANE-PROTEINS; WEB SERVER; CHANNEL; TRANSPORTER; PREDICTION; REVEALS; SITE; TM;

D O I：

10.1093/nar/gks1169

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The PDBTM database (http://pdbtm.enzim.hu), the first comprehensive and up-to-date transmembrane protein selection of the Protein Data Bank, was launched in 2004. The database was created and has been continuously updated by the TMDET algorithm that is able to distinguish between transmembrane and non-transmembrane proteins using their 3D atomic coordinates only. The TMDET algorithm can locate the spatial positions of transmembrane proteins in lipid bilayer as well. During the last 8 years not only the size of the PDBTM database has been steadily growing from similar to 400 to 1700 entries but also new structural elements have been identified, in addition to the well-known alpha-helical bundle and beta-barrel structures. Numerous 'exotic' transmembrane protein structures have been solved since the first release, which has made it necessary to define these new structural elements, such as membrane loops or interfacial helices in the database. This article reports the new features of the PDBTM database that have been added since its first release, and our current efforts to keep the database up-to-date and easy to use so that it may continue to serve as a fundamental resource for the scientific community.

引用

页码：D524 / D529

页数：6

共 31 条

[1] The structures of BtuCD and MscS and their implications for transporter and channel function [J].

Bass, RB ;

Locher, KP ;

Borths, E ;

Poon, Y ;

Strop, P ;

Lee, A ;

Rees, DC .

FEBS LETTERS, 2003, 555 (01) :111-115

[2]

Bateman A, 2004, NUCLEIC ACIDS RES, V32, pD138, DOI [10.1093/nar/gkp985, 10.1093/nar/gkr1065, 10.1093/nar/gkh121]

[3] CGDB: A database of membrane protein/lipid interactions by coarse-grained molecular dynamics simulations [J].

Chetwynd, Alan P. ;

Scott, Kathryn A. ;

Mokrab, Younes ;

Sansom, Mark S. P. .

MOLECULAR MEMBRANE BIOLOGY, 2008, 25 (08) :662-669

[4] A refined structure of human aquaporin-1 [J].

de Groot, BL ;

Engel, A ;

Grubmüller, H .

FEBS LETTERS, 2001, 504 (03) :206-211

[5] Structural themes in ion channels [J].

Doyle, DA .

EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 2004, 33 (03) :175-179

[6] X-ray structure of a CIC chloride channel at 3.0 Å reveals the molecular basis of anion selectivity [J].

Dutzler, R ;

Campbell, EB ;

Cadene, M ;

Chait, BT ;

MacKinnon, R .

NATURE, 2002, 415 (6869) :287-294

[7] Prediction of the human membrane proteome [J].

Fagerberg, Linn ;

Jonasson, Kalle ;

von Heijne, Gunnar ;

Uhlen, Mathias ;

Berglund, Lisa .

PROTEOMICS, 2010, 10 (06) :1141-1149

[8] TMBETA-GENOME:: database for annotated β-barrel membrane proteins in genomic sequences [J].

Gromiha, M. Michael ;

Yabuki, Yukimitsu ;

Kundu, Srinesh ;

Suharnan, Sivasundaram ;

Suwa, Makiko .

NUCLEIC ACIDS RESEARCH, 2007, 35 :D314-D316

[9] TMFunction: database for functional residues in membrane proteins [J].

Gromiha, M. Michael ;

Yabuki, Yukimitsu ;

Suresh, M. Xavier ;

Thangakani, A. Mary ;

Suwa, Makiko ;

Fukui, Kazuhiko .

NUCLEIC ACIDS RESEARCH, 2009, 37 :D201-D204

[10] AstexViewer™:: a visualisation aid for structure-based drug design [J].

Hartshorn, MJ .

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 2002, 16 (12) :871-881

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