I have a sequence of DNA for an oncogene with a novel oncogenic mutation. I want to know how does this mutation affect the structure of the protein produced by that gene. What softwares can help me in this?
You may translate the DNA to amino acid based on human codon usage. Then you have 2 options: 1-put your protein sequence in an online server "I-TASSER" to predict the structure by ab initio modeling. Then you use another server "SAVES v5.0" to validate the predicted structures to choose the best one.
2-Put your protein sequence into the SWISS model server which can predict your structure by homology modeling.
If you have time you may evaluate the stability of your predicted structure my molecular dynamics simulations.