PDBsum: a web-based database of summaries and analyses of all PDB structures

Laskowski, Roman A.; Hutchinson, E. Gail; Michie, Alex; Wallace, Andrew; Jones, Martin L.; Thornton, Janet M.

doi:10.1016/s0968-0004(97)01140-7

Cited by 572 publications

(415 citation statements)

References 19 publications

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“…Table 1 shows the various primary and secondary databases. SCOP (Structural Classification Of Proteins) [6], CATH (Class, Architecture, Topology and Homology) and PDB Sum [7] are the major protein structure classification databases. Table 2 provides information about various available tools for protein structure determination.…”

Section: Bioinformatics Approaches For Structure Analysismentioning

confidence: 99%

Untitled

2017

RJLBPCS

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ABSTRACT:In view of an increased demand for microbial originated Industrial enzymes in a wide variety of fields such as food, dairy, pharmaceutical, detergent, textile, oleo-chemical, perfume and cosmetic industries etc., there is every need to improve the stability, specificity and catalytic efficiencies of the enzymes to obtain better yields which can be possible through protein engineering using various computational methods. Availability of genomic and proteomic sequence databases resulted in an explosion of information which aid in discovering new microbial enzymes whose properties can be improved or modified. The present review mainly focuses on various computational tools for structure prediction (homology modeling) and protein engineering.

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Section: Bioinformatics Approaches For Structure Analysismentioning

confidence: 99%

Untitled

2017

RJLBPCS

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“…Lys39 provides the covalent attachment site for the enzyme's co-factor, pyridoxal 5 0 -phosphate, and Tyr43 forms a hydrogen bond to one of the phosphate oxygen atoms of the co-factor. Interestingly, the left-handed helix forms the core of the (highly conserved) PROSITE (Bairoch & Bucher, 1994) sequence motif characteristic of alanine racemases (V-x-K-A-(DN)-(GA)-Y-G-H-G), which maps to residues Val37 to Gly46 as revealed by PDBsum (Laskowski et al, 1997).…”

Section: Spatial Motif Recognitionmentioning

confidence: 99%

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

Kleywegt

1999

Journal of Molecular Biology

291

240

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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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“…This prediction can be checked by analysis of the conservation of residues involved in the biochemical activity of a protein with a known structure. Two public databases containing information about such residues, PDBsum 24 and PROSITE, 25 were used to define ''function signatures.'' PDBsum is the database of summaries of information about structure from the PDB, available from the UCL Web site.…”

Section: Automatic Functional Sites Checkup: Sitematchmentioning

confidence: 99%

“…PDBsum is the database of summaries of information about structure from the PDB, available from the UCL Web site. 24 PROSITE is a dictionary of protein sites and patterns developed at the University of Geneva. 25 At the same time, most of the structural files are annotated by their authors with annotations identified by specific keywords following PDB guidelines.…”

Section: Automatic Functional Sites Checkup: Sitematchmentioning

confidence: 99%

See 1 more Smart Citation

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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PDBsum: a web-based database of summaries and analyses of all PDB structures

Cited by 572 publications

References 19 publications

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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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