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Residue Contact Prediction for Protein Structure using 2-Norm Distances

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IJCA Proceedings on National Conference on Innovative Paradigms in Engineering and Technology (NCIPET 2012)
© 2012 by IJCA Journal
ncipet - Number 11
Year of Publication: 2012
Authors:
Nikita V. Mahajan
L.G.Malik

Nikita V Mahajan and L.G.Malik. Article: Residue Contact Prediction for Protein Structure using 2-Norm Distances. IJCA Proceedings on National Conference on Innovative Paradigms in Engineering and Technology (NCIPET 2012) ncipet(11):17-21, March 2012. Full text available. BibTeX

@article{key:article,
	author = {Nikita V. Mahajan and L.G.Malik},
	title = {Article: Residue Contact Prediction for Protein Structure using 2-Norm Distances},
	journal = {IJCA Proceedings on National Conference on Innovative Paradigms in Engineering and Technology (NCIPET 2012)},
	year = {2012},
	volume = {ncipet},
	number = {11},
	pages = {17-21},
	month = {March},
	note = {Full text available}
}

Abstract

Bioinformatics is a field which uses technology and is rapidly growing, to solve the problem related to biological area. Study of protein, predicting its structure to know its function is an important field in bioinformatics. Protein unit that is twenty amino acids have total information for converting linear sequences of amino acid into its unique and globular structures. Protein folding problem is process to determine that protein is folding into its exact tertiary structure. Protein folds into matter of seconds to its stable 3-D structure; once it is stable it may perform proper functions. Contact map is an intermediate step for converting 1-d structure to 3-d structure. Contact map is the representative graphical view, how the protein folds into its proper structure. Here, 6 parameters are set, which consider 2-norm distances for generating the contact map. It will consider the co-ordinate data, only of the residue having alpha carbon as contact type and map the contact as 1 if differences is greater than threshold value or -1 if less than threshold value.

References

  • Fernanda Hembecker, HeitorSilvério Lopes (2010), “A Molecular Model for Representing Protein Structures and its Application to Protein Folding” IEEE.
  • NarjesKhatoonHabibi, Mohammad HosseinSaraee (2009), “Protein Contact Map Prediction Based On an Ensemble Learning Method”, In:International Conference on Computer Engineering and Technology.
  • YosiShibberu and Allen Holder (2011), “A Sepctral Approach to Protein Structure Alignment”. In:IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 8, NO. 4.
  • Nitin Gupta, NitinMangal and SomenathBiswas (2004), “Evolution and similarity evaluation of Protein Structures in Contact map space.
  • Giuseppe Tradigo (2009), “On the Integration of Protein Contact Map Predictions”, In:IEEE
  • JingjingHu ,XiaolanShen , Yu Shao , Chris Bystroff , Mohammed J. Zaki (2002), “Mining Protein Contact Maps”, In:Workshop on Data Mining in Bioinformatics
  • Kibeom Park, Michele Vendruscolo, and EytanDomany (2000), “Toward an Energy Function for the Contact Map Representation of Proteins”, In: PROTEINS: Structure, Function, and Genetics 40:237–248
  • ZaferAydin, YucelAltunbasak, and HakanErdogan (2011), “Bayesian Models and Algorithms for Protein B-Sheet Prediction”.In: Transactions on computational biology and bioinformatics, vol. 8, no. 2
  • The Protein Data Bank,” http://www.rcsb.org/pdb, 2009
  • Introduction to protein structure and structural bioinformatics, “secondary-sructure.html”
  • Gabriela Czibula, Maria-IulianaBocicor and Istvan-GergelyCzibula (2000), “A Reinforcement Learning Model for Solving the Folding Problem".
  • Muhammad Asif Khan, Muhammad A. Khan, Zahoor Jan, Hamid Ali and Anwar M. Mirza (2010). “Performance of Machine Learning Techniques in Protein Fold Recognition Problem”. In: IEEE.
  • http://www.ics.uci.edu/~baldig/betasheet_data.html, 2009.