Structural genomics: Computational methods for structure analysis

被引：76

作者：

Goldsmith-Fischman, S ^{[1
]}

Honig, B ^{[1
]}

机构：

[1] Columbia Univ, Howard Hughes Med Inst, Dept Biochem & Mol Biophys, New York, NY 10032 USA

来源：

PROTEIN SCIENCE | 2003年 / 12卷 / 09期

关键词：

structural genomics; homology modeling; structure alignments; functional analysis;

D O I：

10.1110/ps.0242903

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 success of structural genomics initiatives requires the development and application of tools for structure analysis, prediction, and annotation. In this paper we review recent developments in these areas; specifically structure alignment, the detection of remote homologs and analogs, homology modeling and the use of structures to predict function. We also discuss various rationales for structural genomics initiatives. These include the structure-based clustering of sequence space and genome-wide function assignment. It is also argued that structural genomics can be integrated into more traditional biological research if specific biological questions are included in target selection strategies.

引用

页码：1813 / 1821

页数：9

共 134 条

[1] Combining multiple structure and sequence alignments to improve sequence detection and alignment: Application to the SH2 domains of Janus kinases [J].

Al-Lazikani, B ;

Sheinerman, FB ;

Honig, B .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2001, 98 (26) :14796-14801

[2] Automated structure-based prediction of functional sites in proteins: Applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking [J].

Aloy, P ;

Querol, E ;

Aviles, FX ;

Sternberg, MJE .

JOURNAL OF MOLECULAR BIOLOGY, 2001, 311 (02) :395-408

[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] InterPro - an integrated documentation resource for protein families, domains and functional sites [J].

Apweiler, R ;

Attwood, TK ;

Bairoch, A ;

Bateman, A ;

Birney, E ;

Biswas, M ;

Bucher, P ;

Cerutti, L ;

Corpet, F ;

Croning, MDR ;

Durbin, R ;

Falquet, L ;

Fleischmann, W ;

Gouzy, J ;

Hermjakob, H ;

Hulo, N ;

Jonassen, I ;

Kahn, D ;

Kanapin, A ;

Karavidopoulou, Y ;

Lopez, R ;

Marx, B ;

Mulder, NJ ;

Oinn, TM ;

Pagni, M ;

Servant, F ;

Sigrist, CJA ;

Zdobnov, EM .

BIOINFORMATICS, 2000, 16 (12) :1145-1150

[5] ConSurf: An algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information [J].

Armon, A ;

Graur, D ;

Ben-Tal, N .

JOURNAL OF MOLECULAR BIOLOGY, 2001, 307 (01) :447-463

[6] Gene Ontology: tool for the unification of biology [J].

Ashburner, M ;

Ball, CA ;

Blake, JA ;

Botstein, D ;

Butler, H ;

Cherry, JM ;

Davis, AP ;

Dolinski, K ;

Dwight, SS ;

Eppig, JT ;

Harris, MA ;

Hill, DP ;

Issel-Tarver, L ;

Kasarskis, A ;

Lewis, S ;

Matese, JC ;

Richardson, JE ;

Ringwald, M ;

Rubin, GM ;

Sherlock, G .

NATURE GENETICS, 2000, 25 (01) :25-29

[7] PRINTS - A PROTEIN MOTIF FINGERPRINT DATABASE [J].

ATTWOOD, TK ;

BECK, ME .

PROTEIN ENGINEERING, 1994, 7 (07) :841-848

[8]

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

[9] SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics [J].

Bertone, P ;

Kluger, Y ;

Lan, N ;

Zheng, DY ;

Christendat, D ;

Yee, A ;

Edwards, AM ;

Arrowsmith, CH ;

Montelione, GT ;

Gerstein, M .

NUCLEIC ACIDS RESEARCH, 2001, 29 (13) :2884-2898

[10] Pairwise sequence alignment below the twilight zone [J].

Blake, JD ;

Cohen, FE .

JOURNAL OF MOLECULAR BIOLOGY, 2001, 307 (02) :721-735

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