Protein Structure Alignment
Protein Folding Structure Comparison

Two pairs of unlike protein structures, which belong to different categories in the structural classification of protein (SCOP), are compared.  The structure 1M2E is respectively compared with N-terminal domain and C-terminal domain of Chain A of 1A2O (1A2O-A).  The information of structural classification of 1M2E, N-terminal domain and C-terminal domain of 1A2O-A is listed in Table V.  Protein 1M2E and N-terminal domain of 1A2O-A belongs to same class, same fold and same superfamily, but different family in SCOP.  However, protein 1M2E and C-terminal domain of 1A2O-A only belongs to same class, but different fold and superfamily.  It is significant that PFSA-S values indicate the N-terminal domain of 1A2O-A has higher structural similarity with 1M2E than C-terminal domain of 1A2O-A, which agrees with structural classification in SCOP.

The PFSA alignment table in Table VI and Table VII correspondingly shows the alignment of 1M2E with N-terminal domain and C-terminal domain of 1A2O-A.  The sequence-independent alignment mode is applied for these comparisons.  The alignment tables in Table VI and Table VII display how the fragments with similar local folding shapes are matched up with insertion of gaps.  In alignment table, the aligned protein folding shape code with identity is marketed with “|”, the analogue with “*”, the dislike with “^” and the insertion with “+”.  Actually, the alignment table shows the optimized structural alignment with matching all local structural fragments between two proteins.  The PFSA-S provides the quantitative assessment of similarity for global structural comparisons with 1M2E, which is listed in Table V, including the numbers of identity and analog of folding shapes, and the number of insertion gaps.  In contrast to C-terminal domain, the comparison of N-terminal domain of 1A2O-A and 1M2E have higher PFSA-S similarity score, larger number of identical and analogous folding shapes and less number of gaps, which agrees with the difference of two pairs of  structures.




More Applications

Objective Application
Reveal the nature of protein folding variations
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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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