Question: Structural Bioinformatics Approaches To Fix Residues In Dis-Allowed Regions Of Ramachandran Plot
1
gravatar for Khader Shameer
8.6 years ago by
Manhattan, NY
Khader Shameer18k wrote:

I am working on molecular dynamics simulation of a protein structure with approximately 1900 residues. In PDB, only c-alpha trace was available for this protein. I generated full-atom model using the following steps:

  • C-alpha trace is downloaded from PDB
  • Side-chains atoms are generated using MaxSprout
  • Missing atoms added using DeepView

After these 3 steps, I assessed the quality of the structure using PROCHECK via PDBSum and noticed that approximately 3% of the residues are in the disallowed region.

I would like to know the best practice to fix the residues in disallowed region ? Is there any tool or methodology (for example energy minimization) that can adjust the phi-psi values of residues in disallowed region ? I would also like to know if there is any better equivalent for the tools that I have used for side-chain atom generation and fixing the missing atoms.

Looking forward for your suggestions.

pdb protein structure structural • 4.1k views
ADD COMMENTlink modified 8.6 years ago by Anuraj Nayarisseri740 • written 8.6 years ago by Khader Shameer18k

I am generating by hand some PDB structures that only contain alpha carbons, but when I submit them to maxsprout I always get the error "No atom chains found, invalid input file?", what could be the reason? Or, could you paste here somehow files you submitted to maxsprout and which only contain alpha carbons? thankis a lot

ADD REPLYlink written 6.7 years ago by Flow1.5k
2
gravatar for Spitshine
8.6 years ago by
Spitshine640
Esch-sur-Alzette, Luxembourg
Spitshine640 wrote:

I once was told that you are likely to make things worse if you start with EM here (haven't done anything myself in years). How many residues in regular protein structure are in disallowed (or energetically unfavorable) states? 3% does not seem out of this world. Depending on your overall goal, you could leave it as is and proceed with MD. If you have a specific question regarding the molecule it could be answered irrespective of it.

ADD COMMENTlink modified 8.6 years ago • written 8.6 years ago by Spitshine640

Roland thanks a lot for your thoughts. I have 32 residues and most of them are in the loop regions. The overall aim is to map a nsSNP identified in a GWAS to this structure and study the conformational changes induced by the mutation.

ADD REPLYlink written 8.6 years ago by Khader Shameer18k

Roland: thanks a lot for your thoughts. I have 32 residues and most of them are in the loop regions. The overall aim is to map a nsSNP identified in a GWAS to this structure and study the conformational changes induced by the mutation

ADD REPLYlink written 8.6 years ago by Khader Shameer18k
1
gravatar for Anuraj Nayarisseri
8.6 years ago by
Indore
Anuraj Nayarisseri740 wrote:

In Deep view itself you can push this amino acids into the core region by building a loop between above and below amino acids of your target amino acid which is in disallowed region. just follow the below steps.

1) Open your given pdb file in Deep viewer. 2) Go to control panel and color all amino acid in to any single color.i will suggest you to give pink color to the whole structure. 3) Give any particular color for your target amino acid which is in dissallowed region and two amino acids below and two amino acids above of your target amino acid you give some different color.

For example: following are your amino acids in your pdb - 34LYS,35His,36Arg,37Ile,38Pro,etc. say for instance. 36th Arg is in disallowed region. you change the color of 36th Arg into Green color. and 34th and 35th you give red Color. 37th and 38th you give Blue color.

4) Now you see Ramachandran plot once again and confirm that green color amino acid is in disallowed region. ONce you confirm you can build a loop.after confirmation you may close ramachandran plot.

5) Go to Build menu. select "Build loop".now you can see click on 1st anger. 6) Now you click on any anger of 34th or 35th amino acid and then it will ask you click on second anger this time you may click on 37th and 38th amino acid. Immediately confirmation and geometry will change. now you can see the green amino acid will be inside the core region. 7) Once you done with this you may perform Energy Minimization. then you can save the structure.

Hope this will help you.

ADD COMMENTlink written 8.6 years ago by Anuraj Nayarisseri740

Thanks Anuraj. Could you please share a literature support for this procedure ?

ADD REPLYlink written 8.6 years ago by Khader Shameer18k
0
gravatar for Anuraj Nayarisseri
8.6 years ago by
Indore
Anuraj Nayarisseri740 wrote:

Here is the tutorial. http://spdbv.vital-it.ch/loop_tut.html

you can follow those steps which i mentioned in the above post to get it push those amino acids into core region.

ADD COMMENTlink written 8.6 years ago by Anuraj Nayarisseri740

Anuraj: Please add additional points to same answers using 'edit' option or using 'Add Comment' for better readability.

ADD REPLYlink written 8.6 years ago by Khader Shameer18k
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