Tools
These tools were made to address specific needs that arose during day-to-day lab work. These have not been thoroughly tested and do not have a manual, but if you see anything that might be of use to you, feel free to contact me.
Convert NMRview “.xpk” peak list into UCSF Sparky “.list” peak list. Search protein sequences (or any other sequence) for occurrence of motifs, amino acid, protease sites, etc. Can be used to highlight and identify the location of specific amino acid (e.g. all basic/acidic amino acids, all Ser/Thr, etc.) Use this tool to fit binding data. Currently, fitting anisotropy data for a titration to determine binding affinity is supported. This is useful to get fit estimates when there is no access to a data fitting program or script.
Useful if you have a peak list from NMRview and need to view these peaks in Sparky.
Currently only converts lists with up to ~150 peaks, to convert larger peak lists, simply split the list into smaller lists of ~150 peaks.
This tool can also fetch sequences based on a UniProt ID, and search RegEx expressions.
For additional information about the how to determine binding affinity see: How to determine binding affinity.