progress report 24 sept 2010

this week i've just learn the steps how to use autodock in linux with the helps of my friends...
there are differences using autodock in linux and windows....so after this i will try to run docking in linux..

i learn about the chemical structure of various ligands such as 3HB-CoA, 3HV-CoA & 3HHX-CoA....after confirming the structures, i try to prepare the ligand using chemsketch...

besides that, i also read some journals about the mechanism and expression of PHA synthase from chromobacterium sp USM2...

schrodinger 2010

i've successful to get the academic access to log on to schrodinger...

then, i've just downloaded Maestro software and got academic license for it..

now, i'm trying to learn how to use it for docking coz some said that using glide(application in maestro) is easier than autodock....

oh, i forget to tell that last time i used autodock to carry out docking but there are some error that me & femlin & also esther not understand it.....*sigh*

i will try harder to learn & use glide...hope that femlin, esther & Dr.hasni at MBBS will teach me....

MD result for 5 nano seconds

i already got MD result for 5 nano seconds last friday after 3 weeks waiting for it..this structure have minimum energy than the first one...

so, i analyze the structure using SAVES server (structural analysis and verification server).....

and below are the result from the analysis:

ramachandran plot:

• residues in most favoured region : 65.7%
  
• residues in additional allowed region : 29.9%
  
• residues in generously allowed region : 2.4%
  
• residues in dissallowed region : 2.0%
  

errat: 62.474

verify_3D: 67.25%

the result for verify_3D is better than the initial model because the initial model is only 49%.

the result for errat is lower than last one(90.502)

what i'm doing rite now?

currently, i'm doing structure prediction on pha synthase of chromobacterium sp usm2..what i have done are:

1. multiple alignment of pha synthase from various bacteria..

2. secondary structure analysis for this protein..

3. structure prediction of this protein using iTASSER.

4. analysis of all the predicted models to get the best model..using procheck, and others.

5. analysis of hydrophobicity & hydrophilicity of the protein model.

6. i also did the prediction of binding sites of the protein and detect the amino acid at the predicted binding sites.


i will update my progress on the next entry...

bye..

p/s: need to study more on protein structure prediction & analysis coz not fully understand on this topic...

1st entry

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i will tell more about my project on my second entry...
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~bye~