please someone gives me explanation about the HOMOLOGY MODELING.
actually, I have a different 3D model result from Swiss Model and YASARA based on the same sequence and the template is the same too. how could it be?
If you are having a protein sequence and you want to determine its 3D structure homology modeling can be used which models the structure of your sequence based on a template structure. The simplest tool is SPDBV (Swiss-model) that does blast search to find the template structure. According to my knowledge the modeled 3D structures could differ inspite of same template depending being used.
Carbon distribution based homology modeling is hoped to give better results as proteins fold due to carbon along the sequence.
Through Swiss model one can generate a Proteins 3-D model based on the appropriate template identification and can validate it.
To my knowledge, swissmodel constructs a single model from a single alignment, while other softwares are able to construct infinite number of models from a single alignment. The key is always in the alignment.. if there is any differences in the alignment then it will give different models.
The second source for differences is that non-conserved regions are also constructed differently in each software.
simply choose the best model by any scoring method (force field energy, molprobity, procheck, qmean, etc..)
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