There are millions of proteins given in PDB, the sequence for which we can download in FASTA format. There are also hundreds of SNP's given in NCBI dbSNP. My question is whether the proteins in PDB incorporate the SNP's into their structure? If not, is there a way to visualize protein structure using any tool after a SNP on the protein? I know that tools like SIFT exist but they only say whether or not a SNP is harmful or not. They don't comment on the structure of the protein in anyway.
Go for I mutant (http://gpcr2.biocomp.unibo.it/cgi/predictors/I-Mutant3.0/I-Mutant3.0.cgi) you will get the free energy change value and whether the mutation/SNP is stable or not. In order to visualize the structure why don't you submit the SNP containing sequence in online modelling softwares (http://raptorx.uchicago.edu/ ) or try Swiss model.
See variant (or SNP) annotations by:
http://www.cbioportal.org/mutation_mapper.jsp
and/or
http://rbbt.bioinfo.cnio.es/Structure
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