Hi All, I am looking for the best bionformatics tool to predict the protein stability changes upon mutation and I found that there is many tools avail for the same here http://omictools.com/protein-stability-change-prediction-category but I am confused which one need to select because I need a tool with the following criteria:
1.The tool has to support for both sequence and structure for prediction.
2. Need to have standalone version *.
3.Fast and accuracy *.
4. The tool has to predict the stability changes for single mutation, double mutation and combination of mutations (optional).
( I am not sure with this point that calculation of stability changes upon double and combination mutation is possible. So this point can be a optional but it would be better if you suggest some)
Kinldly someone suggest me a best tool with the mentioned criterias would be really helpful for me.
Thanking you in advance
What you demand does not exist! Normally, sequence based tools cannot directly predict stability - they are mostly based on multi-sequence alignment, and work on the assumption that if some residue is highly conserved among an alignment of homologous sequence, there has to be a reason for it - either the residue is directly involved in function or indirectly affects function by being essential for proper folding and stability - In absence of structural data you cannot tell which of the two reasons is responsible for the conservation, although the nature of the residue can give you a hint. The more highly conserved a position is, and the less conservative the substitution is, the higher the likelyhood that this substitution is deleterious. Structure-based algorithms can add to this an analysis of the interaction between neighboring residues and an estimate of the change in interaction energy upon mutation. The most accurate methods combine the two approaches, but are dependent on the availability of well-resolved structural data.
I have worked on this field couple of years ago. Since proteins only have marginal stability, there is no universal rule which can ensure the correctness for all proteins. Rather, using expertised decision based on concensus for different algorithms should be better. The algorithms I have developped included "thermorank", "PROTS-RF". Good luck!
Dear Yungi Li,
Many more thanks for your kind reply and Could you tell me some basic usage ideas of it like tutorial. Especially I want it for PROTS-RF .
Thanking you in advance
What you demand does not exist! Normally, sequence based tools cannot directly predict stability - they are mostly based on multi-sequence alignment, and work on the assumption that if some residue is highly conserved among an alignment of homologous sequence, there has to be a reason for it - either the residue is directly involved in function or indirectly affects function by being essential for proper folding and stability - In absence of structural data you cannot tell which of the two reasons is responsible for the conservation, although the nature of the residue can give you a hint. The more highly conserved a position is, and the less conservative the substitution is, the higher the likelyhood that this substitution is deleterious. Structure-based algorithms can add to this an analysis of the interaction between neighboring residues and an estimate of the change in interaction energy upon mutation. The most accurate methods combine the two approaches, but are dependent on the availability of well-resolved structural data.
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