ProtMot
Welcome to PROTeins MOTif analysis tool.
(See some analysis examples at the bottom of this page)

Enter here one or more PDB ids of published structures to analyze
(find them with or at Proteopedia )

PDB id PDB id PDB id
PDB id PDB id PDB id

and/or upload your own structures in PDB format

PDB file
PDB file
PDB file
PDB file
PDB file
PDB file
and then click

ProtMot, a PROTeins MOTif analysis tool.
This web site analyzes structure of proteins and output the list of hydrogen bonding patterns network motifs. The list of motifs, a superset of the secondary structures, is shown both projected on the protein structure and as a network motif significance profile (SP), a chart which gives the occurrences of each motif in the protein.

In publications, credits should state:
PROTeins MOTif analysis tool (2008), Ofer Rahat, Jaime Prilusky, Yaakov (Koby) Levy, Barak Raveh, Uri Alon and Gideon Schreiber

Selected samples of ProtMot's H-Bonding Network Motif Frequency analysis

  • Hemoglobin Here we compare Hemoglobin significance profile of Maned wolf (1fhj) Deer (1hds) Human (1ird) and Horse (1iwh).
    The SP of homologues protein structures is expected to be similar. Surprisingly, the SP of Deer Hemoglobin (green, pdb 1hds, structure solved to 1.98Å resolution), is highly different from all other mammals (here Human, Maned wolf, and Horse are shown). Globally, the structures of Human hemoglobin and of Deer are highly similar, with RMSD of as low as 0.9Å.

    This suggests that the structure of Deer hemoglobin has local dissimilarities from all the others. Interestingly, a high percentage of this structure is out of the Ramachandran allowed region (below). Concluding, SP revealed local differences between structures, which could be tremendous even when globally the structures seem to be identical.