Manuscript Number : IJSRST162415

Bioinformatics Tools for Protein Analysis

Authors(3) :-Mahin Ghorbani, Fatemeh Ghorbani, Hamed Karimi

Understanding of the relationship between amino acid sequence and three dimensional structure of protein is one of the main objects of bioinformatics, if the relationship is known; it can be helpful for prediction of the protein structure from its amino acid sequence. In this paper, you will learn the fundamentals of structures of proteins, and we will discuss the basic tools and databases for protein visualization and classification. On the basis of such reviews and discussions, you will be able to understand how to predict protein structure and function from its amino acid sequence. The protein structure databases discussed in this paper are such as Protein Data Bank, NCBI Structure Database (MMDB). The Protein structure visualization databases and tools discussed here are such as Cn3-D, Chemscape Chine, Rasmol and Protein Explorer , SWISS PDB Viewer , Mage and Kinemages, and PDBsum. The protein structure alignment discussed are such as VAST and DALI Server. The Domain Architecture databases discussed here are CDD, CDART. Discussed tools for plotting protein-ligand interaction is Ligplot and the protein classification approaches are SCOP and CATH.

Authors and Affiliations

Mahin Ghorbani
Department of Biotechnology, Fergusson College, F.C. Road, Pune, Maharashtra, India
Fatemeh Ghorbani
Centre for continuing education, John Abbott College, Montreal, Quebec, Canada
Hamed Karimi
Department of computer engineering, Azad university of Farsan, Chaharmahal va bakhtiari, Iran

Bioinformatics Tools, Protein Prediction, Protein Visualization, Protein Classification, Protein Function.

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  19. Sillitoe I, Lewis, TE, Cuff AL, Das S, Ashford P, Dawson NL, Furnham N, Laskowski RA, Lee D, Lees J, Lehtinen S, Studer R, Thornton JM, Orengo CA,Nucleic Acids Res. 2015 Jan,CATH: comprehensive structural and functional annotations for genome sequences.
  20. Ghorbani M and Karimi H. Cyclin-Dependent Kinases as valid targets for cancer treatment. Journal of Pharmacy Research 2015,9(6),377-382
  21. Ghorbani M, Karimi H, 'Ion Channels Association with Diseases and their Role as Therapeutic Targets in Drug Discovery', International Journal of Scientific Research in Science and Technology(IJSRST), 1(3):65-69,July-August 2015.
  22. Ghorbani M, Karimi H, 'Role of Aquaporins in Diseases and Drug Discovery', International Journal of Scientific Research in Science and Technology(IJSRST),1(3):60-64, July-August 2015
  23. Mahin Ghorbani, Hamed Karimi, 'Role of G-Protein Coupled Receptors in Cancer Research and Drug Discovery', International Journal of Scientific Research in Science and Technology (IJSRST),1(3), pp.122-126, July-August 2015.
  24. Mahin Ghorbani, Hamed karimi, 'Role of Biomarkers in Cancer Research and Drug Development', International Journal of Scientific Research in Science and Technology(IJSRST),1(3), pp.127-132, July-August 2015
  25. Ghorbani M,Karimi H,Ten Bioinformatics Tools for Single Nucleotide Polymorphisms, American Journal of Bioinformatics ;2014:3(2):45-48
  26. Mahin Ghorbani, Hamed Karimi, 'Bioinformatics Approaches for Gene Finding ', International Journal of Scientific Research in Science and Technology (IJSRST),1(4),12-15, September-October 2015.
  27. Mahin Ghorbani, Hamed Karimi, 'Bioinformatics Methods for Biochemical Pathways and System Biology Analysis', International Journal of Scientific Research in Science and Technology (IJSRST),1(4),75-79, September-October 2015.
  28. Mahin Ghorbani, Hamed Karimi, Role of Biotechnology in cancer control, International Journal of Scientific Research in Science and Technology (IJSRST),,1(5),180-185, November-December 2015
  29. Ghorbani M, Karimi H, 'Role of Microarray Technology in Diagnosis and Classification of Malignant Tumours', International Journal of Scientific Research in Science and Technology(IJSRST), 1(3):117-121, July-August 2015

Publication Details

Published in : Volume 2 | Issue 4 | July-August 2016
Date of Publication : 2016-08-30
License:  This work is licensed under a Creative Commons Attribution 4.0 International License.
Page(s) : 107-111
Manuscript Number : IJSRST162415
Publisher : Technoscience Academy

Print ISSN : 2395-6011, Online ISSN : 2395-602X

Cite This Article :

Mahin Ghorbani, Fatemeh Ghorbani, Hamed Karimi, " Bioinformatics Tools for Protein Analysis", International Journal of Scientific Research in Science and Technology(IJSRST), Print ISSN : 2395-6011, Online ISSN : 2395-602X, Volume 2, Issue 4, pp.107-111, July-August-2016.
Journal URL : https://ijsrst.com/IJSRST162415
Citation Detection and Elimination     |      | |
  • 8Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan 1;42(1):D297-303. Epub 2013 Dec 6. doi: 10.1093/nar/gkt1208.
  • 9Wang Y, Geer LY, Chappey C, Kans JA, Bryant SH. Cn3D: sequence and structure views for Entrez. Trends Biochem Sci. 2000 Jun; 25(6): 300-2. PubMed PMID: 10838572]
  • Guex, N. and Peitsch, M.C. (1997) SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis 18, 2714-2723
  • Richardson, D. C.; J.S. Richardson (January 1992). "The kinemage: a tool for scientific communication". Protein Science 1 (1): 3–9. doi:10.1002/pro.5560010102. PMC 2142077. PMID 1304880.
  • Laskowski RA (Jan 2001). "PDBsum: summaries and analyses of PDB structures". Nucleic Acids Research 29 (1): 221–2. doi:10.1093/nar/29.1.221. PMC 29784. PMID 11125097
  • Gibrat JF, Madej T, Bryant SH. Surprising similarities in structure comparison. Curr Opin Struct Biol. 1996 Jun; 6(3): 377-85.
  • Holm L, Sander C. Dali: a network tool for protein structure comparisonTrends Biochem Sci. 1995 Nov;20(11):478-80.
  • Marchler-Bauer A, Derbyshire MK, Gonzales NR, Lu S, Chitsaz F, Geer LY, Geer RC, He J, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, Marchler GH, Song JS, Thanki N, Wang Z, Yamashita RA, Zhang D, Zheng C, Bryant SH. CDD: NCBI's conserved domain database. Nucleic Acids Res. 2015 Jan 28;43(Database issue):D222-2. doi: 10.1093/nar/gku1221. Epub 2014 Nov 20
  • Geer LY, Domrachev M, Lipman DJ, Bryant SH. CDART: protein homology by domain architecture. Genome Res. 2002 Oct;12(10):1619-23.
  • Wallace A C, Laskowski R A, Thornton J M (1996). LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng., 8, 127-134
  • Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
  • Sillitoe I, Lewis, TE, Cuff AL, Das S, Ashford P, Dawson NL, Furnham N, Laskowski RA, Lee D, Lees J, Lehtinen S, Studer R, Thornton JM, Orengo CA,Nucleic Acids Res. 2015 Jan,CATH: comprehensive structural and functional annotations for genome sequences.
  • Ghorbani M and Karimi H. Cyclin-Dependent Kinases as valid targets for cancer treatment. Journal of Pharmacy Research 2015,9(6),377-382
  • Ghorbani M, Karimi H, 'Ion Channels Association with Diseases and their Role as Therapeutic Targets in Drug Discovery', International Journal of Scientific Research in Science and Technology(IJSRST), 1(3):65-69,July-August 2015.
  • Ghorbani M, Karimi H, 'Role of Aquaporins in Diseases and Drug Discovery', International Journal of Scientific Research in Science and Technology(IJSRST),1(3):60-64, July-August 2015
  • Mahin Ghorbani, Hamed Karimi, 'Role of G-Protein Coupled Receptors in Cancer Research and Drug Discovery', International Journal of Scientific Research in Science and Technology (IJSRST),1(3), pp.122-126, July-August 2015.
  • Mahin Ghorbani, Hamed karimi, 'Role of Biomarkers in Cancer Research and Drug Development', International Journal of Scientific Research in Science and Technology(IJSRST),1(3), pp.127-132, July-August 2015
  • Ghorbani M,Karimi H,Ten Bioinformatics Tools for Single Nucleotide Polymorphisms, American Journal of Bioinformatics ;2014:3(2):45-48
  • Mahin Ghorbani, Hamed Karimi, 'Bioinformatics Approaches for Gene Finding ', International Journal of Scientific Research in Science and Technology (IJSRST),1(4),12-15, September-October 2015.
  • Mahin Ghorbani, Hamed Karimi, 'Bioinformatics Methods for Biochemical Pathways and System Biology Analysis', International Journal of Scientific Research in Science and Technology (IJSRST),1(4),75-79, September-October 2015.
  • Mahin Ghorbani, Hamed Karimi, Role of Biotechnology in cancer control, International Journal of Scientific Research in Science and Technology (IJSRST),,1(5),180-185, November-December 2015
  • Ghorbani M, Karimi H, 'Role of Microarray Technology in Diagnosis and Classification of Malignant Tumours', International Journal of Scientific Research in Science and Technology(IJSRST), 1(3):117-121, July-August 2015
    • " target="_blank"> BibTeX     |
  • 8Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan 1;42(1):D297-303. Epub 2013 Dec 6. doi: 10.1093/nar/gkt1208.
  • 9Wang Y, Geer LY, Chappey C, Kans JA, Bryant SH. Cn3D: sequence and structure views for Entrez. Trends Biochem Sci. 2000 Jun; 25(6): 300-2. PubMed PMID: 10838572]
  • Guex, N. and Peitsch, M.C. (1997) SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis 18, 2714-2723
  • Richardson, D. C.; J.S. Richardson (January 1992). "The kinemage: a tool for scientific communication". Protein Science 1 (1): 3–9. doi:10.1002/pro.5560010102. PMC 2142077. PMID 1304880.
  • Laskowski RA (Jan 2001). "PDBsum: summaries and analyses of PDB structures". Nucleic Acids Research 29 (1): 221–2. doi:10.1093/nar/29.1.221. PMC 29784. PMID 11125097
  • Gibrat JF, Madej T, Bryant SH. Surprising similarities in structure comparison. Curr Opin Struct Biol. 1996 Jun; 6(3): 377-85.
  • Holm L, Sander C. Dali: a network tool for protein structure comparisonTrends Biochem Sci. 1995 Nov;20(11):478-80.
  • Marchler-Bauer A, Derbyshire MK, Gonzales NR, Lu S, Chitsaz F, Geer LY, Geer RC, He J, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, Marchler GH, Song JS, Thanki N, Wang Z, Yamashita RA, Zhang D, Zheng C, Bryant SH. CDD: NCBI's conserved domain database. Nucleic Acids Res. 2015 Jan 28;43(Database issue):D222-2. doi: 10.1093/nar/gku1221. Epub 2014 Nov 20
  • Geer LY, Domrachev M, Lipman DJ, Bryant SH. CDART: protein homology by domain architecture. Genome Res. 2002 Oct;12(10):1619-23.
  • Wallace A C, Laskowski R A, Thornton J M (1996). LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng., 8, 127-134
  • Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
  • Sillitoe I, Lewis, TE, Cuff AL, Das S, Ashford P, Dawson NL, Furnham N, Laskowski RA, Lee D, Lees J, Lehtinen S, Studer R, Thornton JM, Orengo CA,Nucleic Acids Res. 2015 Jan,CATH: comprehensive structural and functional annotations for genome sequences.
  • Ghorbani M and Karimi H. Cyclin-Dependent Kinases as valid targets for cancer treatment. Journal of Pharmacy Research 2015,9(6),377-382
  • Ghorbani M, Karimi H, 'Ion Channels Association with Diseases and their Role as Therapeutic Targets in Drug Discovery', International Journal of Scientific Research in Science and Technology(IJSRST), 1(3):65-69,July-August 2015.
  • Ghorbani M, Karimi H, 'Role of Aquaporins in Diseases and Drug Discovery', International Journal of Scientific Research in Science and Technology(IJSRST),1(3):60-64, July-August 2015
  • Mahin Ghorbani, Hamed Karimi, 'Role of G-Protein Coupled Receptors in Cancer Research and Drug Discovery', International Journal of Scientific Research in Science and Technology (IJSRST),1(3), pp.122-126, July-August 2015.
  • Mahin Ghorbani, Hamed karimi, 'Role of Biomarkers in Cancer Research and Drug Development', International Journal of Scientific Research in Science and Technology(IJSRST),1(3), pp.127-132, July-August 2015
  • Ghorbani M,Karimi H,Ten Bioinformatics Tools for Single Nucleotide Polymorphisms, American Journal of Bioinformatics ;2014:3(2):45-48
  • Mahin Ghorbani, Hamed Karimi, 'Bioinformatics Approaches for Gene Finding ', International Journal of Scientific Research in Science and Technology (IJSRST),1(4),12-15, September-October 2015.
  • Mahin Ghorbani, Hamed Karimi, 'Bioinformatics Methods for Biochemical Pathways and System Biology Analysis', International Journal of Scientific Research in Science and Technology (IJSRST),1(4),75-79, September-October 2015.
  • Mahin Ghorbani, Hamed Karimi, Role of Biotechnology in cancer control, International Journal of Scientific Research in Science and Technology (IJSRST),,1(5),180-185, November-December 2015
  • Ghorbani M, Karimi H, 'Role of Microarray Technology in Diagnosis and Classification of Malignant Tumours', International Journal of Scientific Research in Science and Technology(IJSRST), 1(3):117-121, July-August 2015
    • " target="_blank">RIS     |
  • 8Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan 1;42(1):D297-303. Epub 2013 Dec 6. doi: 10.1093/nar/gkt1208.
  • 9Wang Y, Geer LY, Chappey C, Kans JA, Bryant SH. Cn3D: sequence and structure views for Entrez. Trends Biochem Sci. 2000 Jun; 25(6): 300-2. PubMed PMID: 10838572]
  • Guex, N. and Peitsch, M.C. (1997) SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis 18, 2714-2723
  • Richardson, D. C.; J.S. Richardson (January 1992). "The kinemage: a tool for scientific communication". Protein Science 1 (1): 3–9. doi:10.1002/pro.5560010102. PMC 2142077. PMID 1304880.
  • Laskowski RA (Jan 2001). "PDBsum: summaries and analyses of PDB structures". Nucleic Acids Research 29 (1): 221–2. doi:10.1093/nar/29.1.221. PMC 29784. PMID 11125097
  • Gibrat JF, Madej T, Bryant SH. Surprising similarities in structure comparison. Curr Opin Struct Biol. 1996 Jun; 6(3): 377-85.
  • Holm L, Sander C. Dali: a network tool for protein structure comparisonTrends Biochem Sci. 1995 Nov;20(11):478-80.
  • Marchler-Bauer A, Derbyshire MK, Gonzales NR, Lu S, Chitsaz F, Geer LY, Geer RC, He J, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, Marchler GH, Song JS, Thanki N, Wang Z, Yamashita RA, Zhang D, Zheng C, Bryant SH. CDD: NCBI's conserved domain database. Nucleic Acids Res. 2015 Jan 28;43(Database issue):D222-2. doi: 10.1093/nar/gku1221. Epub 2014 Nov 20
  • Geer LY, Domrachev M, Lipman DJ, Bryant SH. CDART: protein homology by domain architecture. Genome Res. 2002 Oct;12(10):1619-23.
  • Wallace A C, Laskowski R A, Thornton J M (1996). LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng., 8, 127-134
  • Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
  • Sillitoe I, Lewis, TE, Cuff AL, Das S, Ashford P, Dawson NL, Furnham N, Laskowski RA, Lee D, Lees J, Lehtinen S, Studer R, Thornton JM, Orengo CA,Nucleic Acids Res. 2015 Jan,CATH: comprehensive structural and functional annotations for genome sequences.
  • Ghorbani M and Karimi H. Cyclin-Dependent Kinases as valid targets for cancer treatment. Journal of Pharmacy Research 2015,9(6),377-382
  • Ghorbani M, Karimi H, 'Ion Channels Association with Diseases and their Role as Therapeutic Targets in Drug Discovery', International Journal of Scientific Research in Science and Technology(IJSRST), 1(3):65-69,July-August 2015.
  • Ghorbani M, Karimi H, 'Role of Aquaporins in Diseases and Drug Discovery', International Journal of Scientific Research in Science and Technology(IJSRST),1(3):60-64, July-August 2015
  • Mahin Ghorbani, Hamed Karimi, 'Role of G-Protein Coupled Receptors in Cancer Research and Drug Discovery', International Journal of Scientific Research in Science and Technology (IJSRST),1(3), pp.122-126, July-August 2015.
  • Mahin Ghorbani, Hamed karimi, 'Role of Biomarkers in Cancer Research and Drug Development', International Journal of Scientific Research in Science and Technology(IJSRST),1(3), pp.127-132, July-August 2015
  • Ghorbani M,Karimi H,Ten Bioinformatics Tools for Single Nucleotide Polymorphisms, American Journal of Bioinformatics ;2014:3(2):45-48
  • Mahin Ghorbani, Hamed Karimi, 'Bioinformatics Approaches for Gene Finding ', International Journal of Scientific Research in Science and Technology (IJSRST),1(4),12-15, September-October 2015.
  • Mahin Ghorbani, Hamed Karimi, 'Bioinformatics Methods for Biochemical Pathways and System Biology Analysis', International Journal of Scientific Research in Science and Technology (IJSRST),1(4),75-79, September-October 2015.
  • Mahin Ghorbani, Hamed Karimi, Role of Biotechnology in cancer control, International Journal of Scientific Research in Science and Technology (IJSRST),,1(5),180-185, November-December 2015
  • Ghorbani M, Karimi H, 'Role of Microarray Technology in Diagnosis and Classification of Malignant Tumours', International Journal of Scientific Research in Science and Technology(IJSRST), 1(3):117-121, July-August 2015
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