[11] Applying motif and profile searches

Bork, Peer; Gibson, Toby J.

doi:10.1016/s0076-6879(96)66013-3

Cited by 150 publications

(86 citation statements)

References 36 publications

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“…Iterative collection of the PP2C family members: An alignment of the PP2C members annotated in PROSITE (Bairoch & Bucher, 1994; entry PS01032) was the starting point for iterative sequence homology searches using several pattern search methods (for details of the strategy see Bork & Gibson, 1996). After each iteration, newly detected sequences were added to the alignment using CLUSTALW (Thompson et al, 1994).…”

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confidence: 99%

The protein phosphatase 2C (PP2C) superfamily: Detection of bacterial homologues

et al. 1996

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Abstract:A thorough sequence analysis of the various members of the eukaryotic protein serinekhreonine phosphatase 2C (PP2C) family revealed the conservation of 11 motifs. These motifs could be identified in numerous other sequences, including fungal adenylate cyclases that are predicted to contain a functionally active PP2C domain, and a family of prokaryotic serine/ threonine phosphatases including SpoIIE. Phylogenetic analysis of all the proteins indicates a widespread sequence family for which a considerable number of isoenzymes can be inferred.

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confidence: 99%

The protein phosphatase 2C (PP2C) superfamily: Detection of bacterial homologues

et al. 1996

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“…Clearly, spatial motif recognition has the potential to become a powerful tool in structural analysis, just as sequence motif recognition is important in the analysis of sequence databases (Bork & Gibson, 1996). SPASM is a rapid, intuitive, and user-friendly tool to quickly identify proteins that display structural similarities at the level of residues, and that perhaps have (or once had) unsuspected functional similarities.…”

Section: Resultsmentioning

confidence: 99%

Recognition of spatial motifs in protein structures 1 1Edited by J. Thornton

Kleywegt

1999

Journal of Molecular Biology

291

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As the structural database continues to expand, new methods are required to analyse and compare protein structures. Whereas the recognition, comparison, and classi®cation of folds is now more or less a solved problem, tools for the study of constellations of small numbers of residues are few and far between. In this paper, two programs are described for the analysis of spatial motifs in protein structures. The ®rst, SPASM, can be used to ®nd the occurrence of a motif consisting of arbitrary main-chain and/or side-chains in a database of protein structures. The program also has a unique capability to carry out``fuzzy pattern matching'' with relaxed requirements on the types of some or all of the matching residues. The second program, RIGOR, scans a single protein structure for the occurrence of any of a set of pre-de®ned motifs from a database. In one application, spatial motif recognition combined with pro®le analysis enabled the assignment of the structural and functional class of an uncharacterised hypothetical protein in the sequence database. In another application, the occurrence of short left-handed helical segments in protein structures was investigated, and such segments were found to be fairly common. Potential applications of the techniques presented here lie in the analysis of (newly determined) structures, in comparative structural analysis, in the design and engineering of novel functional sites, and in the prediction of structure and function of uncharacterised proteins.

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“…4,15 The method extends the idea of a generalized sequence-profile alignment 16,17 to profile-profile alignments. A similar procedure is used in the LAMA prediction server.…”

Section: Sequence Comparison: Psi-blast and Basic The Profile-to-promentioning

confidence: 99%

The Helicobacter pylori genome: From sequence analysis to structural and functional predictions

et al. 1999

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Fold assignments for proteins from the Helicobacter pylori genome are carried out using BASIC, a profile-profile alignment algorithm recently tested on the Mycoplasma genitalium and Escherichia coli genomes. The fold assignments are followed by automated function evaluation, based on the multilevel description of functional sites in proteins. Over 40% of the proteins encoded in the H. pylori genome can be recognized as belonging to a protein family with known structure. Previous estimates suggested that only 10-15% of genome proteins could be characterized this way. This dramatic increase in the number of recognized homologies between H. pylori proteins and structurally characterized protein families is partly due to the rapid increase of the database of known protein structures, but mostly it is due to the significant improvement in prediction algorithms. Knowledge of a protein fold adds a new dimension to our understanding of its function and, similarly, structure prediction can also add to understanding, verification, and/or prediction of function for uncharacterized proteins. Several examples analyzed in more detail in this article illustrate insights that can be achieved from structure and detailed function prediction. Proteins 1999;36:20-30.1999 Wiley-Liss, Inc.

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[11] Applying motif and profile searches

Cited by 150 publications

References 36 publications

The protein phosphatase 2C (PP2C) superfamily: Detection of bacterial homologues

The protein phosphatase 2C (PP2C) superfamily: Detection of bacterial homologues

Recognition of spatial motifs in protein structures 1 1Edited by J. Thornton

The Helicobacter pylori genome: From sequence analysis to structural and functional predictions

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