Thomas Waksman

I used HHBlits via the MPI website If I submit whole protein sequence - 10000 matches, mostly kinase proteins, and the alignment is to a subsection of the query. If...

negative bits score

5

I have observed negative bits score for some pairs of protein structures in an all-against-all comparison of a collection of structures. I don't understand how this is possible, because Smith-Waterman...

MGnify database hits not found on MGnify website

7

Using the FoldSeek website, many of the hits with highest bit score are from the MGnify database, but using either the identifier (MGYP + digits) or protein sequence I am...

I think databases are much larger than the FoldSeek program, and my institute would not support downloading multiple TBs of databases. Furthermore, PDBeFold or DALI websites allow uploading multiple .pdb...

Could you please suggest a method to compare the contact map to an AlphaFold prediction? If I understand correctly, the default TT3D output contact map is a matrix of length(protein1)*length(protein2)...