All of this can be done through either Windows or Linux.
Next, what you will want to do is a multiple sequence alignment or a pair-wise sequence alignment between the proteins. Depending on if you want to know how each sequence compares to a master sequence (pair-wise) or how each sequence compares to each other(Multiple)
Multiple sequence alignment: http://www.ebi.ac.uk/Tools/msa/clustalo/
These will let you know the % similarity, generally how similar the sequences are to each other.
If you do not have structures for these proteins you can use SWISS MODEL to generate a homology mode if a suitablely similar structure is found: http://swissmodel.expasy.org/
Next download VMD: http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD
Load your PDB structures up in VMD: File-> New molecule
Ok now make it all look presentable by going to:
Ok now make it all look presentable by going to:
Graphics->Representations
Drawing Method and choose New Cartoon
Coloring Method Choose ColorID and choose a color
Do this for each protein by using the Selected molecule dropdown box at the top of the Representations window.
Once you have all the structures done
Goto: Extensions -> Analysis-> RMSD calculator
Where is says "residue 5 to 85" change that to the length or your protein. If you don't know the exact length goto: Extensions-> Analysis->Sequence viewer. Try and use as much of the structure as possible or if the region you are interested in is > 20 residues try that first. Next in the RMSD window click Align then click RMSD. RMSD is the Root Mean Square Deviation, basically how different overall the two structures by their positions in 3D space. Low number is good, high number is bad.
Look at the spot where you think the substrate of molecule interacts with the protein(press keyboard S to scale the 3D models, R to rotate and T to translate) and identify the residues by using:
Mouse->Label->Atoms and click on the structure it should give you a residue number and atom name the residue number should be something like "R57"
Go back to the protein sequence alignments and look around these atoms and see if the residues are the same or similar.
If the residues are the same or similar and the RMSD between the structures is small there is a good chance the proteins bind or interact with the same substrate.
If the residues are the same or similar and the RMSD between the structures is small there is a good chance the proteins bind or interact with the same substrate.
More complex analysis can then be done with Molecular Dynamics and docking simulations.
If you have more specific questions or errors please let me know and I will see what I can do to help.
On Tue, Oct 8, 2013 at 2:45 PM, John Dohnal <johnhdohnal@aol.com> wrote:
Hi Josiah,
Maybe if I told you what I wanted to do, you could better advise me on which program/s might be better for what I want to do. I have a target molecule as a substrate. By identifying several structures in the molecule, I've identified a number of proteins which have substrates which are similar to the structures in my target molecule. I want to, first, compare the homology of these proteins to find any similar structures. Second, I'd like to be able to "clip" those similar structures and be able to "paste" them together. Lastly, I'd like to see how well the "new" protein fits with my original target molecule. I realize that I will probably need several programs to accomplish this, so if you could explain how each program could perform each portion of my process, that would be awesome.
Thanks,
John
On Thursday, September 19, 2013 9:59:12 PM UTC-4, Josiah Zayner wrote:The code appears broke beyond brokenness. The website is down http://proteinshop.lbl.gov/Index.html. I would try emaling Sylvia at SNCrivelli [at] lbl.gov if you really want to try and get it working. However.If you want to do similar stuff I would install VMD http://www.ks.uiuc.edu/Research/vmd/or pymol: sudo apt-get install pymolfor secondary structure prediction try PSIPRED: http://bioinf.cs.ucl.ac.uk/psipred/And for protein structure prediction use: http://swissmodel.expasy.org/ if it has some homology to some other structureor http://godzilla.uchicago.edu/cgi-bin/aashish2/TerItFix/TerItFix.cgi if it does not have any homologyfor Molecular Dynamics Simulations try namd which comes with VMD or gromacs: sudo apt-get install gromacs
On Thursday, September 19, 2013 7:46:59 AM UTC-5, John Dohnal wrote:I have never used a Linux OS before, but I downloaded the latest version of Ubuntu in order to run Protein Shop. I downloaded the latest version of Protein Shop, but I don't know how to start it. I know nothing about using Linux, so any explicit, basic instructions would be most helpful. In the readme file, it mentions some other files that may need to be installed, but I don't even know where to begin. Please help!Thanks,JohnTo view this discussion on the web visit https://groups.google.com/d/msgid/diybio/8e149ea2-2171-43a0-8941-3997f3d26a4c%40googlegroups.com.--
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