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Literature DB >> 9399828

The Signal Recognition Particle Database (SRPDB).

Abstract

This release of the SRPDB (signal recognition particle database, http://pegasus.uthct.edu/SRPDB/SRPDB . html ) adds four SRP RNA sequences (a total of 99 SRP RNA sequences), 23 SRP protein sequences (a total of 63 protein sequences from SRP9, SRP14, SRP19, SRP21, SRP54, SRP68 or SRP72), and, for the first time, sequences of the alpha subunit of the eukaryotic SRP receptor and its homologous bacterial proteins (a total of 21 sequences). Sequences are offered phylogenetically ordered, annotated with links to the primary databases, and in aligned form. Also downloadable are sample SRP RNA secondary structure diagrams, three-dimensional models of representative SRP RNAs, and search motifs.

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Year: 1998 PMID： 9399828 PMCID： PMC147211 DOI： 10.1093/nar/26.1.177

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

11 in total

1. A truncated isoform of Ca2+/calmodulin-dependent protein kinase II expressed in human islets of Langerhans may result from trans-splicing.

Authors: M A Breen; S J Ashcroft
Journal: FEBS Lett Date: 1997-06-16 Impact factor: 4.124

2. Basic local alignment search tool.

Authors: S F Altschul; W Gish; W Miller; E W Myers; D J Lipman
Journal: J Mol Biol Date: 1990-10-05 Impact factor: 5.469

3. SRP-RNA sequence alignment and secondary structure.

Authors: N Larsen; C Zwieb
Journal: Nucleic Acids Res Date: 1991-01-25 Impact factor: 16.971

4. The EMBL nucleotide sequence database.

Authors: G Stoesser; M A Moseley; J Sleep; M McGowran; M Garcia-Pastor; P Sterk
Journal: Nucleic Acids Res Date: 1998-01-01 Impact factor: 16.971

5. Comparative analysis of tertiary structure elements in signal recognition particle RNA.

Authors: C Zwieb; F Müller; N Larsen
Journal: Fold Des Date: 1996

Review 6. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Authors: S F Altschul; T L Madden; A A Schäffer; J Zhang; Z Zhang; W Miller; D J Lipman
Journal: Nucleic Acids Res Date: 1997-09-01 Impact factor: 16.971

7. The RDP (Ribosomal Database Project).

Authors: B L Maidak; G J Olsen; N Larsen; R Overbeek; M J McCaughey; C R Woese
Journal: Nucleic Acids Res Date: 1997-01-01 Impact factor: 16.971

8. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

Authors: J D Thompson; D G Higgins; T J Gibson
Journal: Nucleic Acids Res Date: 1994-11-11 Impact factor: 16.971

9. Model for signal sequence recognition from amino-acid sequence of 54K subunit of signal recognition particle.

Authors: H D Bernstein; M A Poritz; K Strub; P J Hoben; S Brenner; P Walter
Journal: Nature Date: 1989-08-10 Impact factor: 49.962

10. Homology of 54K protein of signal-recognition particle, docking protein and two E. coli proteins with putative GTP-binding domains.

Authors: K Römisch; J Webb; J Herz; S Prehn; R Frank; M Vingron; B Dobberstein
Journal: Nature Date: 1989-08-10 Impact factor: 49.962

20 in total

1. Structure of the phylogenetically most conserved domain of SRP RNA.

Authors: U Schmitz; S Behrens; D M Freymann; R J Keenan; P Lukavsky; P Walter; T L James
Journal: RNA Date: 1999-11 Impact factor: 4.942

2. Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization.

Authors: David H Mathews
Journal: RNA Date: 2004-08 Impact factor: 4.942

The Signal Recognition Particle Database (SRPDB).

1. A truncated isoform of Ca2+/calmodulin-dependent protein kinase II expressed in human islets of Langerhans may result from trans-splicing.

2. Basic local alignment search tool.

3. SRP-RNA sequence alignment and secondary structure.

4. The EMBL nucleotide sequence database.

5. Comparative analysis of tertiary structure elements in signal recognition particle RNA.

Review 6. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

7. The RDP (Ribosomal Database Project).

8. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

9. Model for signal sequence recognition from amino-acid sequence of 54K subunit of signal recognition particle.

10. Homology of 54K protein of signal-recognition particle, docking protein and two E. coli proteins with putative GTP-binding domains.

1. Structure of the phylogenetically most conserved domain of SRP RNA.

2. Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization.

3. ProbKnot: fast prediction of RNA secondary structure including pseudoknots.

4. Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences.

5. Thermodynamic characterization of RNA 2 × 3 nucleotide internal loops.

6. Thermodynamic characterization of naturally occurring RNA tetraloops.

7. Improved RNA secondary structure prediction by maximizing expected pair accuracy.

8. Conformation of 4.5S RNA in the signal recognition particle and on the 30S ribosomal subunit.

9. Isolation of a novel member of small G protein superfamily and its expression in colon cancer.

10. Secondary structure models of the 3' untranslated regions of diverse R2 RNAs.