We used the fold recognition server Phyre (Protein Homology/analogY Recognition Engine 2, http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi id=index) to predict in silico the 3D structure of the three AtMDL monomers.
The similarity between the newly identified C-terminal module and NTs was further explored in the pdb70 structural library using the fold-recognition algorithm HHPred in local and global mode.
In order to identify the optimal set of template structures for modeling of HEN1, we used the fold-recognition (FR) approach, which allows to assess the compatibility of the target sequence with the available protein structures based not only on the sequence similarity, but also on the structural considerations (match of secondary structure elements, compatibility of residue-residue contacts, etc).
FFAS (Jaroszewski et al. 2011), HHpred (Soding et al. 2005), and Phyre2 (Kelley and Sternberg 2009) were used in the fold recognition analysis to detect a proper model for homology modeling.
A representative from each sequence cluster at a certain threshold is selected from each TOCCATA profile to generate a FUGUE profile file, which is used by the fold recognition program FUGUE (19) for homology searches.
In particular, we should be able to deal with them using the same algorithm, regardless whether they are represented as binary vectors, real vectors on different scales, sequences, graph data, etc. Various approaches based on features extracted from protein sequence and often machine learning approaches have been used to tackle the fold recognition problem.
For each of these top families, we carried out a more sensitive profile profile sequence search against the Protein Data Bank (PDB) using HHsearch (Söding, 2005) and the fold recognition method SPARKS-X (Yang et al., 2011).
The fold recognition methods were used https://genesilico.pl/meta2/.
3) The sequence of Thermotoga maritima was added following the fold recognition alignment produced by HHPred [ 39] using the Protein data Bank structure 1mrz.
