Literature DB >> 23982150

PDB@: an offline toolkit for exploration and analysis of PDB files.

Udayakumar Mani1, Sadhana Ravisankar, Sai Mukund Ramakrishnan.   

Abstract

Protein Data Bank (PDB) is a freely accessible archive of the 3-D structural data of biological molecules. Structure based studies offers a unique vantage point in inferring the properties of a protein molecule from structural data. This is too big a task to be done manually. Moreover, there is no single tool, software or server that comprehensively analyses all structure-based properties. The objective of the present work is to develop an offline computational toolkit, PDB@ containing in-built algorithms that help categorizing the structural properties of a protein molecule. The user has the facility to view and edit the PDB file to his need. Some features of the present work are unique in itself and others are an improvement over existing tools. Also, the representation of protein properties in both graphical and textual formats helps in predicting all the necessary details of a protein molecule on a single platform.

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Year:  2013        PMID: 23982150     DOI: 10.1007/s10969-013-9162-x

Source DB:  PubMed          Journal:  J Struct Funct Genomics        ISSN: 1345-711X


  6 in total

1.  Multiple sequence alignment with the Clustal series of programs.

Authors:  Ramu Chenna; Hideaki Sugawara; Tadashi Koike; Rodrigo Lopez; Toby J Gibson; Desmond G Higgins; Julie D Thompson
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

2.  A novel approach to segregate and identify functional loop regions in protein structures using their Ramachandran maps.

Authors:  Mattaparthi Venkata Satish Kumar; Rajaram Swaminathan
Journal:  Proteins       Date:  2010-03

3.  Conscript: RasMol to PyMOL script converter.

Authors:  Scott E Mottarella; Mario Rosa; Abdul Bangura; Herbert J Bernstein; Paul A Craig
Journal:  Biochem Mol Biol Educ       Date:  2010-11       Impact factor: 1.160

4.  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

5.  A simple method for displaying the hydropathic character of a protein.

Authors:  J Kyte; R F Doolittle
Journal:  J Mol Biol       Date:  1982-05-05       Impact factor: 5.469

6.  The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data.

Authors:  Helen Berman; Kim Henrick; Haruki Nakamura; John L Markley
Journal:  Nucleic Acids Res       Date:  2006-11-16       Impact factor: 16.971

  6 in total

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