Bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins

We describe here an energy based computer software suite for narrowing down the search space of tertiary structures of small globular proteins. The protocol comprises eight different computational modules that form an automated pipeline. It combines physics based potentials with biophysical filters...

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Detalles Bibliográficos
Autores principales: Jayaram, B., Bhushan, Kumkum, Shenoy, Sandhya R., Narang, Pooja, Bose, Surojit, Agrawal, Praveen, Sahu, Debashish, Pandey, Vidhu
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2006
Materias:
Computational Biology
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1693886/
https://www.ncbi.nlm.nih.gov/pubmed/17090600
http://dx.doi.org/10.1093/nar/gkl789
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author Jayaram, B.
Bhushan, Kumkum
Shenoy, Sandhya R.
Narang, Pooja
Bose, Surojit
Agrawal, Praveen
Sahu, Debashish
Pandey, Vidhu
author_facet Jayaram, B.
Bhushan, Kumkum
Shenoy, Sandhya R.
Narang, Pooja
Bose, Surojit
Agrawal, Praveen
Sahu, Debashish
Pandey, Vidhu
author_sort Jayaram, B.
collection PubMed
description We describe here an energy based computer software suite for narrowing down the search space of tertiary structures of small globular proteins. The protocol comprises eight different computational modules that form an automated pipeline. It combines physics based potentials with biophysical filters to arrive at 10 plausible candidate structures starting from sequence and secondary structure information. The methodology has been validated here on 50 small globular proteins consisting of 2–3 helices and strands with known tertiary structures. For each of these proteins, a structure within 3–6 Å RMSD (root mean square deviation) of the native has been obtained in the 10 lowest energy structures. The protocol has been web enabled and is accessible at .
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spelling pubmed-16938862006-12-28 Bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins Jayaram, B. Bhushan, Kumkum Shenoy, Sandhya R. Narang, Pooja Bose, Surojit Agrawal, Praveen Sahu, Debashish Pandey, Vidhu Nucleic Acids Res Computational Biology We describe here an energy based computer software suite for narrowing down the search space of tertiary structures of small globular proteins. The protocol comprises eight different computational modules that form an automated pipeline. It combines physics based potentials with biophysical filters to arrive at 10 plausible candidate structures starting from sequence and secondary structure information. The methodology has been validated here on 50 small globular proteins consisting of 2–3 helices and strands with known tertiary structures. For each of these proteins, a structure within 3–6 Å RMSD (root mean square deviation) of the native has been obtained in the 10 lowest energy structures. The protocol has been web enabled and is accessible at . Oxford University Press 2006-12 2006-11-07 /pmc/articles/PMC1693886/ /pubmed/17090600 http://dx.doi.org/10.1093/nar/gkl789 Text en © 2006 The Author(s)
spellingShingle Computational Biology
Jayaram, B.
Bhushan, Kumkum
Shenoy, Sandhya R.
Narang, Pooja
Bose, Surojit
Agrawal, Praveen
Sahu, Debashish
Pandey, Vidhu
Bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins
title Bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins
title_full Bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins
title_fullStr Bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins
title_full_unstemmed Bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins
title_short Bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins
title_sort bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins
topic Computational Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1693886/
https://www.ncbi.nlm.nih.gov/pubmed/17090600
http://dx.doi.org/10.1093/nar/gkl789
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