bioinformatics- the protein already have crystal structure protein. should we follow the same method as homology modelling? or we can use directly protein from pdb without doing homology modelling using swiss-model and do validation 3D protein to make sure the rmsd of protein.
think it is better to use crystal structure of protein. if there is no X-ray or it has very low resolution it will be possible to use homology modeling.
Homolgy modelling is done if crystal structure is not available. In your case as the crystal syructure is available, you can use it. You can model the loops, missing residues & validate it using tools/programs such as Modeller.
Thank you Dr. Rajesh i will try. Actually in my case i dont havr crystal structre protein. I have to use homology modelling tools to buildup my 3D protein but it just shown 40% sequence similarity with the template protein..
if your protein has 40% sequence similarly with template then you can easily generate homology of your protein of interest. SwissModel is easy to use for generating homology model.
But before subsequent use of generated homology model validation step is very important.
If the protein of interest already has an experimentally determined structure, then 'geometry optimization' is necessary in cases such as the following:
1. The available structure has missing atoms or segments, e.g., loops or termini
2. The available structure may have been obtained with a leader peptide, and further studies may require the native protein sequence
3. It may be a low resolution structure
4. If the structure is to be used for any purpose that involves computation of energy - (e.g., studies of dynamics, in silico binding studies, or effects of mutations) then the model obtained by 'restrained energy minimization/SA' should be used. The reasons are:
a) in most cases the X-ray diffraction studies cannot locate hydrogen atoms precisely
b) the experimental structure usually has a very high energy with most contemporary force fields, which could create problems is calculating changes in energy during subsequent studies.
Hi
Even if the cristal structure is known modelling can be ysed to predict the conformational changes of the molecule for example under different physico-chemical conditions.
Check the resolution at which the protein is crystallized that will give you some confidence on using it for further in silico studies. Also check for the completeness of the crystal structure. If any missing residues, missing side chains is observed then model those alone and do restrained minimization.
Hello
If the Crystal structure is available, you can use:
CASTp, Autodock vina, Swissmodel, Qsite, Chimera, RasMol or JMOL, MOE, BIOVIA Discovery Studio.
Check in these links. It might help you.
https://www.click2drug.org/
Good Luck.
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