This version of Structome generates rigid protein structure alignment using GESAMT. The pairwise structure comparison scores are converted to distances and neighbour-joining trees can be visualized and downloaded.
Structome-TM
Structome-TM differs significantly from Structome-Q.
Foldseek based protein structure comparisons are used to compute TM-scores which are then used to generate neighbour-joining
trees as opposed to Q-score. The primary motivation for use of this metric is to think about the local and global sequence
alignment methods in sequence-based phylognetics. Structome-Q, using Q-score is to be thought of as a global structural
alignment program and Structome-TM is a local one.
HMMStruct v1.0
In case if a protein structure has missing SCOP, CATH and ECOD classifications, this can be used to predict those.
HMMology3D v1.0
Interested in finding homologs of your protein structure? Structure-based HMMs have been shown to outperform classical pairwise comparison methods. Give it a try?
Foldseek 3D-to-3Di
The foldseek program allows for encoding of 3D amino acid coordinate data to a 3Di alphabet. The app allows users to explore the 3D structure and its 3Di representative seqeunce.