Can anyone tell me how to find a model for MR? If I start with a sequence alignment, how do I find out which target has a structure that has been solved? vs if I start with a search in PDB, how do I find out which target has the highest sequence identity to my protein?
Do I need to prepare the model before I use it for MR?
Can I combine multiple models for MR?
Thanks.
Dear Gengnam
you can simply perform a BLAST search (for example at the NCBI site) just selecting the PDB as database.
You can see an example at the minute 8 of the following video tutorial
https://www.blogger.com/video.g?token=AD6v5dyPGWsbPCAGPM4bhC7qrFmUL9TIfeArxzSqZ-ao_K6iC3z597YtqkSB2QIvBIxy9TVU52O9By7lhSuO-TFmnmd1-xRgRxnhW6uEon8lV-Lk-zMV2mZq1MT0o4gwaT38-wIRIIY
uploaded on my blog: ProteoCool (https://proteocool.blogspot.com/p/index.html)
good luck
Manuele
A neat trick:
Submit your sequence to SwissModel (https://swissmodel.expasy.org/interactive) and choose the "Search for Templates" options. This gives you a ranked list, sequence and 3D alignment of up to 50 best templates, ranked and annotated for resolution, oligomerization and presence or absence of ligands. The most suitable template for homology modelling of your sequence is also likely to be the best search model for molecular replacement.
dear gengnam li
if you have protein sequences, you should align them with BLAST (in NCBI) or other alignment tools or directly enter the sequence data into the protein modeling server, such as SWISS-MODEL, Phyre2 (http://www.sbg.bio.ic.ac.uk/~phyre2/html/page.cgi?id=index) or others. The result will show a template that matches the protein sequence that we have.
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