Wyniki wyszukiwania

1

Investigation of the applicability range of protein threading software

100%

Jaworski S., Sikorska C.

Current Topics in Biophysics. Supplement

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2011

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tom 34

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nr A: Posters

2

Prediction of signal peptides in protein sequences by neural networks

88%

Plewczynski D., Slabinski L., Ginalski K., Rychlewski L.

Acta Biochimica Polonica

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2008

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tom 55

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nr 2

261-267

We present here a neural network-based method for detection of signal peptides (abbreviation used: SP) in proteins. The method is trained on sequences of known signal peptides extracted from the Swiss-Prot protein database and is able to work separately on prokaryotic and eukaryotic proteins. A query protein is dissected into overlapping short sequence fragments, and then each fragment is analyzed with respect to the probability of it being a signal peptide and containing a cleavage site. While the accuracy of the method is comparable to that of other existing prediction tools, it provides a significantly higher speed and portability. The accuracy of cleavage site prediction reaches 73% on heterogeneous source data that contains both prokaryotic and eukaryotic sequences while the accuracy of discrimination between signal peptides and non-signal peptides is above 93% for any source dataset. As a consequence, the method can be easily applied to genome-wide datasets. The software can be downloaded freely from http://rpsp.bioinfo. pl/RPSP.tar.gz.

3

Repeat region of Brugia malayi sheath protein (Shp-1) carries Dominant B epitopes recognized in filarial endemic population

75%

Jawaharlal J. P. P., Madhumathi J., Prince R. P., Kaliraj P.

Acta Parasitologica

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2014

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tom 59

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nr 3

Transmission of lymphatic filariasis is mediated through microfilariae (L1 stage of the parasite) which is encased in an eggshell called sheath. The sheath protein Shp-1 stabilizes the structure due to the unique repeat region with Met-Pro-Pro-Gln-Gly sequences. Microfilarial proteins could be used as transmission blocking vaccines. Since the repeat region of Shp-1 was predicted to carry putative B epitopes, this region was used to analyze its reactivity with clinical samples towards construction of peptide vaccine. In silico analysis of Shp-1 showed the presence of B epitopes in the region 49–107. The polypeptide epitopic region Shp-149–107 was cloned and expressed in Escherichia coli. Antibody reactivity of the Shp-149–107 construct was evaluated in filarial endemic population by ELISA. Putatively immune endemic normals (EN) showed significantly high reactivity (P < 0.05) when compared to all the other categories. Antibody reactivity of Shp-1 repeat region was similar to that of whole protein proving that this region carries B epitopes responsible for its humoral response in humans. Thus this can be employed for inducing anti-microfilarial immunity in the infected population that may lead to reduction in transmission intensity and also it could be used along with other epitopes from different stages of the parasite in order to manage the disease effectively.

4

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In silico prediction and characterization of three-dimensional structure of actin-1 of Arabidopsis thaliana

75%

Sahu M., Dehury B., Sarmah R., Sahoo S., Sahu J., Sarma K., Sen P., Modi M. K., Barooah M.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2013

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tom 94

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nr 4

Actin-1 is a ubiquitous protein belonging to the reproductive class of Actin family in Arabidopsis thaliana . This protein is involved in the formation of filaments that are major components of the cytoskeleton. Despite the importance of this protein, very little information is available regarding its structure and function in plants. In this study, analysis of the protein sequence was done and comparative model of Actin-1 was constructed (UNIPROT ID: P0CJ46) from Arabidopsis thaliana using the crystal structure of Dictyostelium discoideum actin (PDB ID: 1NLV-A) as template employing Modeller version 9.9. The stable structure was generated by 5 nanosecond molecular dynamics simulation steps using GROMOS43A1 96 force field that characterized its structural and dynamic feature. The biochemical function of the final simulated structure was also investigated using PROFUNC. The molecular simulation study suggested that the modeled Actin-1 protein retain its stable conformation in aqueous solution. The predicted binding sites in the modeled Actin-1 protein are very informative for further protein-ligand interaction study.

5

Identification of amino acid sequences via X-ray crystallography: a mini review of case studies

75%

Pietrzyk A. J., Bujacz A., Jaskolski M., Bujacz G.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2013

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tom 94

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nr 1

6

MIPS sequences: a promising molecular consideration in angiosperm phylogeny and systematics

75%

Hazra A., Nandy P., Sengupta C., Das S.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2018

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tom 99

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nr 1

7

Sequencing and functional analysis of the yeast genome

75%

Zagulski M., Herbert C. J., Rytka J.

Acta Biochimica Polonica

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1998

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tom 45

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nr 3

The genome of the yeast Saccharomyces cerevisiae was sequenced by an international consortium of laboratories from Europe, Canada, the U.S.A. and Japan. This project is now finished and the complete sequence of the first eukaryotic genome was released to the public data bases in April 1996. An overview and preliminary analysis of the entire genome sequence was presented in a special issue of Nature in May 1997, entitled "The yeast genome directory". At its origin the Yeast Genome Sequencing Project provoked much debate and controversy; however, the final results obtained and the insights this has given us into the organisation and content of a eukaryotic genome have more than justified the expectations of the supporters of the project. The importance of genomic sequencing and analysis, especially of model organisms, is now widely accepted and this has resulted in the birth of the new science of genomics (Botstein & Cherry, Proc. Natl. Acad. Sci. U.S.A. 94, 5506, 1997). The information from gene and protein sequences ultimately lead to functional description of all genes. The main strategies describing possible ways to analyse the function of new genes that have been identified by systematic sequencing of Saccharomyces cerevisiae genome are described.

8

Codon recognition by tRNA

63%

Olejniczak M.

Biotechnologia

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2009

|

nr 1

59-64

Ograniczanie wyników

Investigation of the applicability range of protein threading software

Prediction of signal peptides in protein sequences by neural networks

Repeat region of Brugia malayi sheath protein (Shp-1) carries Dominant B epitopes recognized in filarial endemic population

In silico prediction and characterization of three-dimensional structure of actin-1 of Arabidopsis thaliana

Identification of amino acid sequences via X-ray crystallography: a mini review of case studies

MIPS sequences: a promising molecular consideration in angiosperm phylogeny and systematics

Sequencing and functional analysis of the yeast genome

Codon recognition by tRNA