Conformation Analysis
Comparison of 25 Conformers

Here 25 conformers of protein 1M2F (PDB ID) in Fig. 2(A) are compared with 1M2E in Fig. 2(B) which is average structural models of 25 conformers.  These structures have same sequence with higher degree of similar in conformation. 

The PFSA-S is the score of similarity, which is obtained with number of identical and analogous folding shapes and number of gaps, which are listed in above table.

The PFSA alignment table is displayed in Table IV according the rank of PFSA-S in Table III.  The alignment table demonstrates that the PFSA approach does not only align the secondary structure (font with red and blue colors), but it also exhibits the attributes of tertian structure (font with black color).  The font with pink color indicates the location of perturbation inside the secondary structure or the soft shape transfer on terminus of secondary structure.  Actually, the alignment table is obviously to show which local fragments of residues are structural stability or flexibility.   For example, the conformation of fragment with residues (82-106) is more elastic than other local structures.  Although these conformers have very close structural similarity, however, the PFSA approach has ability to differentiate each conformer with its appropriate sensitivity.



More Applications

Objective Application
Reveal the nature of protein folding variations
Mutation vs. change in folding conformation
Antibody (Rituximab) of CD20 fingerprint
Antibody optimization by fingerprint
Design peptide for a specific folding conformation
Comparison of protein conformations
Expose similarity and dissimilarity for conformers
Comparison between Insulin Receptor and IGF-1 Receptor
Misfolding in Amyloid Beta-42
Similarity score for conformation search
ATP Binding Sites on Kinases
Predict multiple protein targets for drug


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