• Journal of Innovative Optical Health Sciences
  • Vol. 11, Issue 2, 1850002 (2018)
Pan Wang1、2, Guangxiao Yang1, and Guangyuan He1、*
Author Affiliations
  • 1The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
  • 2College of Electronics and Information Engineering, South-Central University for Nationalities, Wuhan 430074, P. R. China
  • show less
    DOI: 10.1142/s1793545818500025 Cite this Article
    Pan Wang, Guangxiao Yang, Guangyuan He. PDBlocal: A web-based tool for local inspection of biological macromolecular 3D structures[J]. Journal of Innovative Optical Health Sciences, 2018, 11(2): 1850002 Copy Citation Text show less
    References

    [1] J. L. Moreland, A. Gramada, O. V. Buzko, Q. Zhang, P. E. Bourne, “The Molecular Biology Toolkit (MBT): A modular platform for developing molecular visualization applications,” BMC Bioinform. 6, 21 (2005).

    [2] W. R. Taylor, “Protein knots and fold complexity: Some new twists,” Comput. Biol. Chem. 31, 151–162 (2007).

    [3] H. Huang, A. Sarai, “Analysis of the relationships between evolvability, thermodynamics, and the functions of intrinsically disordered proteins/regions,” Comput. Biol. Chem. 41, 51–57 (2012).

    [4] C. Andreini, I. Bertini, G. Cavallaro, R. J. Najmanovich, J. M. Thornton, “Structural analysis of metal sites in proteins: Non-heme iron sites as a case study,” J. Mol. Biol. 388, 356–380 (2009).

    [5] M. Hernandez, D. Ghersi, R. Sanchez, “SITEHOUND-web: A server for ligand binding site identification in protein structures,” Nucleic Acids Res. 37, W413–W416 (2009).

    [6] C.-H. Tai, V. Sam, J.-F. Gibrat, J. Garnier, P. J. Munson, B. Lee, “Protein domain assignment from the recurrence of locally similar structures,” Proteins 79, 853–866 (2011).

    [7] T. B. Masood, S. Sandhya, N. Chandra, V. Natarajan, “CHEXVIS: A tool for molecular channel extraction and visualization,” BMC Bioinform. 16, 119 (2015).

    [8] H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, P. E. Bourne, “The Protein Data Bank,” Nucleic Acids Res. 28, 235–242 (2000).

    [9] H. Berman, K. Henrick, H. Nakamura, “Announcing the worldwide Protein Data Bank,” Nat. Struct. Biol. 10, 980 (2003).

    [10] T. Can, Y. Wang, Y. F. Wang, J. Su, “FPV: Fast Protein Visualization Using Java 3DTM,” Bioinformatics 19, 913–922 (2003).

    [11] C. Bajaj, P. Djeu, V. Siddavanahalli, A. Thane, TexMol: Interactive visual exploration of large flexible multi-component molecular complexes, Proc. Ann. IEEE Visualization Conf., Los Alamitos: IEEE Computer Society, Austin TX USA, pp. 243–250 (2004).

    [12] H. J. Bernstein, “Recent changes to RasMol, recombining the variants,” Trends Biochem. Sci. 25, 453–455 (2000).

    [13] N. Guex, M. C. Peitsch, “SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling,” Electrophoresis 18, 2714–2723 (1997).

    [14] Y. Wang, L. Y. Geer, C. Chappey, J. A. Kans, S. H. Bryant, “Cn3D: Sequence and structure views for Entrez,” Trends Biochem. Sci. 25, 300–302 (2000).

    [15] A. Herr-aez, “Biomolecules in the computer: Jmol to the rescue,” Biochem. Mol. Biol. Educ. 34, 255–261 (2006).

    [16] W. Humphrey, A. Dalke, K. Schulten, “VMD: Visual molecular dynamics,” J. Mol. Graph. 14, 33–38 (1996).

    [17] E. F. Pettersen, T. D. Goddard, C. C. Huang, G. S. Couch, D. M. Greenblatt, E. C. Meng, T. E. Ferrin, “UCSF Chimera — A visualization system for exploratory research and analysis,” J. Comput. Chem. 25, 1605–1612 (2004).

    [18] P. Emsley, B. Lohkamp, W. G. Scott, K. Cowtan, “Features and development of Coot,” Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).

    [19] M. J. Hartshorn, “AstexViewer: A visualisation aid for structure-based drug design,” J. Comput. Aided Mol. Des. 16, 871–881 (2002).

    [20] R. M. Hanson, J. Prilusky, Z. Renjian, T. Nakane, J. L. Sussman, “JSmol and the next-generation webbased representation of 3D molecular structure as applied to Proteopedia,” Israel J. Chem. 53, 207–216 (2013).

    [21] A. S. Rose, P. W. Hildebrand, “NGL Viewer: A web application for molecular visualization,” Nucleic Acids Res. 43, W576–W579 (2015).

    [22] H. Li, K.-S. Leung, T. Nakane, M.-H. Wong, “iview: An interactive WebGL visualizer for protein–ligand complex,” BMC Bioinform. 15, 56 (2014).

    [23] G.-J. Bekker, H. Nakamura, A. R. Kinjo, “Molmil: A molecular viewer for the PDB and beyond,” J. Cheminform. 8, 42 (2016).

    [24] S. I. O'Donoghue, K. S. Sabir, M. Kalemanov, C. Stolte, B. Wellmann, V. Ho, M. Roos, N. Perdigo, F. A. Buske, J. Heinrich, B. Rost, A. Schafferhans, “Aquaria: Simplifying discovery and insight from protein structures,” Nat. Methods 12, 98–99 (2015).

    [25] E. Boutet, D. Lieberherr, M. Tognolli, M. Schneider, P. Bansal, A. J. Bridge, S. Poux, L. Bougueleret, I. Xenarios, “UniProtKB/Swiss-Prot, the manually annotated section of the UniProt KnowledgeBase: How to use the entry view,” Methods Mol. Biol. 1374, 23–54 (2016).

    [26] F. Mwalongo, M. Krone, G. Reina, T. Ertl, “Stateof- the-art report in web-based visualization,” Comput. Graph. Forum 35, 553–575 (2016).

    [27] M. Carson, C. E. Bugg, “Algorithm for ribbon models of proteins,” J. Mol. Graph. 4, 121–122 (1986).

    [28] A. Barbato, P. Benkert, T. Schwede, A. Tramontano, J. Kosinski, “Improving your target-template alignment with MODalign,” Bioinformatics 28, 1038–1039 (2012).

    [29] C. H. Ngan, D. R. Hall, B. Zerbe, L. E. Grove, D. Kozakov, S. Vajda, “FTSite: High accuracy detection of ligand binding sites on unbound protein structures,” Bioinformatics 28, 286–287 (2012).

    Pan Wang, Guangxiao Yang, Guangyuan He. PDBlocal: A web-based tool for local inspection of biological macromolecular 3D structures[J]. Journal of Innovative Optical Health Sciences, 2018, 11(2): 1850002
    Download Citation