Provean, MutPred and SNP&GO fail to prediction of the effects nsSNPs coding nonstandard amino acids in the protein sequences. During homology modelling too, the non-standard amino acid were either removed automatically by the modelling tools or the protein sequences (coding non-standard amino acid) was not accepted at all.
Kindly advice on how to address this problem.
Computational Methods to Work as First-Pass Filter in Deleterious SNP Analysis of Alkaptonuria
http://dx.doi.org/10.1100/2012/738423
Dear Friend you can find this paper as useful
Hello Pramod.. thank you for sharing your valued publication. I will surely go through the same.
I found this platform ' "PEPstrMOD: structure prediction of peptides containing natural, non-natural and modified residues" and I wish to explore the same. If successful this should help in the modeling but still clueless about how to predict if an SNP is protective or deleterious when it codes for a non-standard amino acid
have a look at this paper
http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-13-S4-S4
also if you work woth glide you can compute it energy change manualy
https://www.schrodinger.com/kb/733
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