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An interactive 3D viewer of molecules compatible with the suite of ANTHEPROT programs
Unité Bases Moléculaires et Structurales des Systèmes Infectieux, UMR 5086 CNRS, Université Claude Bernard Lyon 1, Lyon, France
- 1 Unité Bases Moléculaires et Structurales des Systèmes Infectieux, UMR 5086 CNRS, Université Claude Bernard Lyon 1, Lyon, France
Journal of Biophysical Chemistry·Volume 03 (2012)·Pages 35–38·Published 15 February 2012·DOI10.4236/jbpc.2012.31004
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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.
KeywordsProteinSequence AnalysisStructural BioinformaticsSoftware3D Structures
- 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
- 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
- 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
- Hanson, R.M. (2008). Jmol: An open-source Java viewer for chemical structures in 3D. http://www.jmol.org/
- 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
- 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
- Catherinot, V. and Labesse, G. (2004) ViTO: Tool for refinement of protein sequence-structure alignments. Bioinformatics, 20, 3694-3696. doi:10.1093/bioinformatics/bth429
- Fournier, D. and Andrade-Navarro, M.A. (2011) PDB-paint, a visualization webservice to tag protein structures with sequence annotations. Bioinformatics, 27, 2605- 2606.
- Cipriano, G., Wesenberg, G., et al., (2011) GRAPE: Graphical abstracted protein explorer. Nucleic Acids Research, 38, W595-W601. doi:10.1093/nar/gkq398
- 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
- 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
- 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.
- Deleage, G., Clerc, F.F. and Roux, B. (1989) Antheprot: IBM PC and Apple macintosh versions. Computer Applications in the Biosciences, 5, 159-160.
- 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