I want to draw 3D structure of Viral protein but don't have idea about it. if someone could help.
Use a 3D-rendering program that understands protein structure! Then you can just read in the coordinates from the protein database (www.rcsb.org) and select the type of standard protein representation you like. For simple visualisation, PyMol is currently one of the best choices, you can get a free educational version from http://www.pymol.org. Other choices are Jmol (http://jmol.sourceforge.net), UCSF chimera (https://www.cgl.ucsf.edu/chimera/) , Discovery studio visualizer (http://accelrys.com/products/collaborative-science/biovia-discovery-studio/visualization-download.php), swiss pub viewer (http://accelrys.com/products/collaborative-science/biovia-discovery-studio/visualization-download.php) are other choices, by no means an exhaustive list.
The online macromolecular museum has some great exhibits and tutorials on virus protein 3D structure.
http://earth.callutheran.edu/Academic_Programs/Departments/BioDev/omm/exhibits.htm
http://earth.callutheran.edu/Academic_Programs/Departments/BioDev/omm/jsmol/hivrt/hivrt.html
What you mean "draw"? If you mean to represente a 3D coordinates from an existing file (such as a PDB file), Annemarie Honegger give you the answer. Other choices are YASARAview which is quite intuitive and if you want some more pro, VMD is a better choice
At the first Brian Thomas Foleys suggestion is right.
by the way I recommend you at the first change your nucleotides to aa by (http://web.expasy.org/translate/) ththen use swissmodeling (http://swissmodel.expasy.org/), Copy your amino acids in start modelling of this website.
Good luck with your work.
Hi Swati. There are many approaches about visualization of 3D-protein structures. It depends on how much information you've had. If you have all-atom coordinates, you can use VMD (Visual Molecular Dynamics), developed by uiuc, to show them. But if you only have sequence information, you may need some online servers to determine its possible 3D structure at first.
Good luck.^_^
do you mean predict 3D structure?
if it is what you mean your first step is to check your target protein sequence in uniprot.org/ database which will provide you with FASTA format for your sequence, second thing use MODDLER or any other bioinformatic tool that available to predict your 3D structure then after that you can follow what has been suggested above. Geethu Suman think this will help you also
UCSF Chimera program (https://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html) is very useful in your case.
Of course, the go-to place for known 3D structures of entire viruses is http://viperdb.scripps.edu , the Virus Particle Explorer DB
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