I am trying to calculate several descriptors for some proteins. I am not a biologist, so maybe I am missing something, regarding the input files.
For instance, if I calculate the geometrical descriptors (MarvinSketch) of HUMAN INSULIN, using as input file the FASTA from http://www.ncbi.nlm.nih.gov/protein/4557671?report=fasta or the MOLFILE (http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:5931) , the Dreiding energy, van der Waals volume, length perpendicular to max and min area are different. The same with other, simpler, descriptor.
These discrepancies, are due alone to different molecules that the files represent? Meaning that the human insulin could have different (slightly) sequences? OR is there any type of file more advisable to be uploaded? fasta or mol, smile..
Any help is welcome, sorry if the problem is purely biologic, and I'm a engineer..