I am looking for the software or API like predicting quantitative parameters(e.g.IC50) expressing drug resistance of various HIV sequences?
In vitro is different from in Vivo. So, it is useless.
Hi Ryosaku,
what you need is at least two things: The 'wildtype' IC50 and a fold resistance.
1) there are various tools for genotype to phenotype mapping (this is probably what you are looking for). What this predicts from your sequence is a fold resistance (fold increase in IC50) for each available drug.
Try http://www.geno2pheno.org/
there is also a 'rule-based'/expert curated tool at Stanford, but it's predictive power is less than the tool above.
2) 'Wildtype' IC50 values can be found in e.g. Shen et al (2008). Nat Med 14(7), pages 762ff...check the tables in the supplementary material. These parameters were measured in primary human PBM cells. That is pretty useful. But be aware of a detail: some compounds tested are highly protein bound and in the assay they used 50% human serum only. So, one needs to correct for protein binding to obtain a good in vivo estimate. That can easily be done, but please tell if you do not know how.
3) Be aware that all these tools oversimplify. E.g. epistasis will not be accounted for. So the result cannot be assumed to be accurate/absolutely quantitative.
Hope that helps a bit...
Max
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