Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database

被引：67

作者：

Tung, Chi-Hua

Huang, Jhang-Wei

Yang, Jinn-Moon

机构：

[1] Natl Chiao Tung Univ, Inst Bioinformat, Hsinchu 30050, Taiwan

[2] Natl Chiao Tung Univ, Dept Biol Sci & Technol, Hsinchu 30050, Taiwan

[3] Natl Chiao Tung Univ, Core Facil Struct Bioinformat, Hsinchu 30050, Taiwan

来源：

GENOME BIOLOGY | 2007年 / 8卷 / 03期

关键词：

D O I：

10.1186/gb-2007-8-3-r31

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

We present a novel protein structure database search tool, 3D- BLAST, that is useful for analyzing novel structures and can return a ranked list of alignments. This tool has the features of BLAST ( for example, robust statistical basis, and effective and reliable search capabilities) and employs a kappa-alpha (kappa, alpha) plot derived structural alphabet and a new substitution matrix. 3D- BLAST searches more than 12,000 protein structures in 1.2 s and yields good results in zones with low sequence similarity.

引用

收藏

页数：16

相关论文

共 59 条

[1] Direct observation of photolysis-induced tertiary structural changes in hemoglobin [J].

Adachi, S ;

Park, SY ;

Tame, JRH ;

Shiro, Y ;

Shibayama, N .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2003, 100 (12) :7039-7044

[2]

Altschul SF, 1996, METHOD ENZYMOL, V266, P460

[3] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].

Altschul, SF ;

Madden, TL ;

Schaffer, AA ;

Zhang, JH ;

Zhang, Z ;

Miller, W ;

Lipman, DJ .

NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402

[4] BASIC LOCAL ALIGNMENT SEARCH TOOL [J].

ALTSCHUL, SF ;

GISH, W ;

MILLER, W ;

MYERS, EW ;

LIPMAN, DJ .

JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410

[5] SCOP database in 2004: refinements integrate structure and sequence family data [J].

Andreeva, A ;

Howorth, D ;

Brenner, SE ;

Hubbard, TJP ;

Chothia, C ;

Murzin, AG .

NUCLEIC ACIDS RESEARCH, 2004, 32 :D226-D229

[6] Rapid 3D protein structure database searching using information retrieval techniques [J].

Aung, Z ;

Tan, KL .

BIOINFORMATICS, 2004, 20 (07) :1045-1052

[7] ATOMIC COORDINATES FOR TRIOSE PHOSPHATE ISOMERASE FROM CHICKEN MUSCLE [J].

BANNER, DW ;

BLOOMER, AC ;

PETSKO, GA ;

PHILLIPS, DC ;

WILSON, IA .

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 1976, 72 (01) :146-155

[8] HELIX GEOMETRY IN PROTEINS [J].

BARLOW, DJ ;

THORNTON, JM .

JOURNAL OF MOLECULAR BIOLOGY, 1988, 201 (03) :601-619

[9]

Bateman A, 2002, NUCLEIC ACIDS RES, V30, P276, DOI [10.1093/nar/gkr1065, 10.1093/nar/gkp985, 10.1093/nar/gkh121]

[10] 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

← 1 2 3 4 5 6 →