Výsledky vyhledávání

A comparative study of sequence- and structure-based features of small RNAs and other RNAs of bacteria

Autor: Amita Barik, Santasabuj Das

Publikováno v: RNA Biology. 15:95-103

Small RNAs (sRNAs) in bacteria have emerged as key players in transcriptional and post-transcriptional regulation of gene expression. Here, we present a statistical analysis of different sequence- and structure-related features of bacterial sRNAs to

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9f87cf857e2ba5b6abf16b9b3c9db626
https://doi.org/10.1080/15476286.2017.1387709

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Hydration of protein–RNA recognition sites

Autor: Ranjit Prasad Bahadur, Amita Barik

Publikováno v: Nucleic Acids Research

We investigate the role of water molecules in 89 protein–RNA complexes taken from the Protein Data Bank. Those with tRNA and single-stranded RNA are less hydrated than with duplex or ribosomal proteins. Protein–RNA interfaces are hydrated less th

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cd37e4395b0f09689f6a3b0f765c3acf
https://doi.org/10.1093/nar/gku679

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PRince: a web server for structural and physicochemical analysis of Protein-RNA interface

Autor: Amita Barik, Abhishek Mishra, Ranjit Prasad Bahadur

Publikováno v: Nucleic Acids Research

We have developed a web server, PRince, which analyzes the structural features and physicochemical properties of the protein-RNA interface. Users need to submit a PDB file containing the atomic coordinates of both the protein and the RNA molecules in

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ec798363bf71e8084437f88ba1f00186
http://europepmc.org/articles/PMC3394290

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A repressor activator protein1 homologue from an oleaginous strain of Candida tropicalis increases storage lipid production in Saccharomyces cerevisiae

Autor: Amita Barik, Atrayee Chattopadhyay, Ranjit Prasad Bahadur, Prabuddha Dey, Mrinal K. Maiti

Publikováno v: FEMS Yeast Research. 15

The r epressor a ctivator p rotein1 (Rap1) has been studied over the years as a multifunctional regulator in Saccharomyces cerevisiae . However, its role in storage lipid accumulation has not been investigated. This report documents the identificatio

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::53a87e4f23becdd761a96e7705c696ae
https://doi.org/10.1093/femsyr/fov013

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Molecular architecture of protein-RNA recognition sites

Autor: Ranjit Prasad Bahadur, Chandran Nithin, Smita P. Pilla, Amita Barik

Publikováno v: Journal of biomolecular structuredynamics. 33(12)

The molecular architecture of protein-RNA interfaces are analyzed using a non-redundant dataset of 152 protein-RNA complexes. We find that an average protein-RNA interface is smaller than an average protein-DNA interface but larger than an average pr

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a41390fabb3290ff7752cafa93f900de
https://pubmed.ncbi.nlm.nih.gov/25562181

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A protein-RNA docking benchmark (I): nonredundant cases

Autor: Ranjit Prasad Bahadur, Chandran Nithin, P Manasa, Amita Barik

Publikováno v: Proteins. 80(7)

We have developed a nonredundant protein–RNA docking benchmark dataset, which is derived from the available bound and unbound structures in the Protein Data Bank involving polypeptide and nucleic acid chains. It consists of nine unbound–unbound c

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4c57bafb3a58140ea5ffaa4147e699f9
https://pubmed.ncbi.nlm.nih.gov/22488669

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Probing binding hot spots at protein–RNA recognition sites

Autor: Sunandan Mukherjee, Ranjit Prasad Bahadur, Amita Barik, Chandran Nithin, Naga Bhushana Rao Karampudi

Publikováno v: Nucleic Acids Research

We use evolutionary conservation derived from structure alignment of polypeptide sequences along with structural and physicochemical attributes of protein-RNA interfaces to probe the binding hot spots at protein-RNA recognition sites. We find that th

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::47f05702a570e137a2272d06b5e4b6f7
http://europepmc.org/articles/PMC4737170

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Identification of single exon genes and their encoded proteins in rice (Oryza sativa L.) genome: an in silico approach

Autor: Ashutosh Kumar, Ambarish Sharan Vidyarthi, Dev Mani Pandey, Amita Barik, Megha Kumari

Publikováno v: International Journal of Bioinformatics Research and Applications. 7:376

In this study, we predicted Single Exon Genes (SEGs) distributed in whole rice genome and their expressed proteins. Complete genome of rice was retrieved from TIGR. CDS annotation in the FEATURE (GenBank format) was used to predict SEGs sequences. Or

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::59af5cb108c5afef5dbab9d827360df9
https://doi.org/10.1504/ijbra.2011.043769

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