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An interactive 3D viewer of molecules compatible with the suite of ANTHEPROT programs

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DOI: 10.4236/jbpc.2012.31004    5,763 Downloads   13,077 Views   Citations

ABSTRACT

In this paper, I will describe a completely new 3D module which can be called from within the well known ANTHEPROT program devoted to protein sequences analysis. This module allows fully interactive handling of high-quality 3D structures with various modes of representation (CA sticks, wireframe, ball and sticks, spacefill mod-els as well as surface, ribbons, Ramachandran plots). Alternatively, ANTHEPROT 3D can be used as an external program fully independant from the global package. It is available from the download page of the web site (http://antheprot-pbil.ibcp.fr/). More than 2800 downloads last year were recorded since the program was delivered.

Cite this paper

Deléage, G. (2012) An interactive 3D viewer of molecules compatible with the suite of ANTHEPROT programs. Journal of Biophysical Chemistry, 3, 35-38. doi: 10.4236/jbpc.2012.31004.

References

[1] Pettersen, E.F., Goddard, T.D., Huang, C.C., et al., (2004) UCSF chimera—A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25, 1605-1612. doi:10.1002/jcc.20084
[2] Sayle, R.A. and Milnerwhite, E.J. (1995) Rasmol—Biomolecular graphics for all. Trends in Biochemical Sciences, 20, 374-376. doi:10.1016/S0968-0004(00)89080-5
[3] Guex, N. and Peitsch, M.C. (1997) SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis, 18, 2714-2723. doi:10.1002/elps.1150181505
[4] Hanson, R.M. (2008). Jmol: An open-source Java viewer for chemical structures in 3D. http://www.jmol.org/
[5] Humphrey, W., Dalke, A. and Schulten, K. (1996) VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14, 33-38. doi:10.1016/0263-7855(96)00018-5
[6] Chavent, M., Levy, B. and Maigret, B. (2008) MetaMol: High-quality visualization of molecular skin surface. Journal of Molecular Graphics & Modelling, 27, 209-216. doi:10.1016/j.jmgm.2008.04.007
[7] Catherinot, V. and Labesse, G. (2004) ViTO: Tool for refinement of protein sequence-structure alignments. Bioinformatics, 20, 3694-3696. doi:10.1093/bioinformatics/bth429
[8] Fournier, D. and Andrade-Navarro, M.A. (2011) PDB-paint, a visualization webservice to tag protein structures with sequence annotations. Bioinformatics, 27, 2605- 2606.
[9] Cipriano, G., Wesenberg, G., et al., (2011) GRAPE: Graphical abstracted protein explorer. Nucleic Acids Research, 38, W595-W601. doi:10.1093/nar/gkq398
[10] Sasin, J.M. and Bujnicki, J.M. (2004) COLORADO3D, a web server for the visual analysis of protein structures. Nucleic Acids Research, 32, W586-W589. doi:10.1093/nar/gkh440
[11] Li, W.Z. and Godzik, A. (2006) VISSA: A program to visualize structural features from structure sequence alignment. Bioinformatics, 22, 887-888. doi:10.1093/bioinformatics/btl019
[12] Deleage, G., Clerc, F.F., Roux, B. and Gautheron, D.C. (1988) Antheprot: A package for protein-sequence analysis using a microcomputer. Computer Applications in the Biosciences, 4, 351-356.
[13] Deleage, G., Clerc, F.F. and Roux, B. (1989) Antheprot: IBM PC and Apple macintosh versions. Computer Applications in the Biosciences, 5, 159-160.
[14] Geourjon, C., Deleage, G. and Roux, B. (1991) Antheprot: An Interactive graphics software for analyzing protein structures from sequences. Journal of Molecular Graphics, 9, 188-190. doi:10.1016/0263-7855(91)80008-N
[15] Geourjon, C. and Deleage, G. (1995) Antheprot: A software to display and analyze 3d nmr structures. Journal of Trace and Microprobe Techniques, 13, 337-338.
[16] Geourjon, C. and Deleage, G. (1995) Antheprot-2.0: A 3-dimensional module fully coupled with protein-sequence analysis-methods. Journal of Molecular Graphics, 13, 209-212. doi:10.1016/0263-7855(95)00035-5
[17] Deleage, G., Combet, C., Blanchet, C. and Geourjon, C. (2001) ANTHEPROT: An integrated protein sequence analysis software with client/server capabilities. Computers in Biology and Medicine, 31, 259-267. doi:10.1016/S0010-4825(01)00008-7
[18] Combet, C., Blanchet, C., Geourjon, C. and Deleage, G. (2000) NPS@: Network protein sequence analysis. Trends in Biochemical Sciences, 25, 147-150. doi:10.1016/S0968-0004(99)01540-6
[19] Sanner, M.F., Olson, A.J. and Spehner, J.C. (1996) Reduced surface: An efficient way to compute molecular surfaces. Biopolymers, 38, 305-320. doi:10.1002/(SICI)1097-0282(199603)38:3<305::AID-BIP4>3.0.CO;2-Y
[20] Kraulis, P.J. (1991) Molscript: A program to produce both detailed and schematic plots of protein structures. Journal of Applied Crystallography, 24, 946-950. doi:10.1107/S0021889891004399
[21] Kabsch, W. and Sander, C. (1983) Dictionary of protein secondary structure—Pattern-recognition of hydrogen- bonded and geometrical features. Biopolymers, 22, 2577-2637. doi:10.1002/bip.360221211
[22] Rocchia, W., Alexov, E. and Honig, B. (2001) Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions. Journal of Physical Chemistry B, 105, 6507-6514. doi:10.1021/jp010454y
[23] Word, J.M., Lovell, S.C., Richardson, J.S. and Richardson, D.C. (1999) Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation. Journal of Molecular Biology, 285, 1735- 1747. doi:10.1006/jmbi.1998.2401

  
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