Protein tertiary structure defines its functions, classification and binding sites. Similar structural characteristics between two proteins often lead to the similar characteristics thereof. Determining structural similarity accurately in real time is a crucial research issue. In this paper, we present a novel and effective scoring scheme that is dependent on novel features extracted from protein alpha carbon distance matrices. Our scoring scheme is inspired from pattern recognition and computer vision. Our method is significantly better than the current state of the art methods in terms of family match of pairs of protein structures and other statistical measurements. The effectiveness of our method is tested on standard benchmark structures. A web service is available at this http URL where you can get the similarity measurement score between two protein structures based on our method.
@cite_25: Here, we present MultiProt, a fully automated highly efficient technique to detect mul- tiple structural alignments of protein structures. MultiProt finds the common geometrical cores be- tween input molecules. To date, most methods for multiple alignment start from the pairwise align- ment solutions. This may lead to a small overall alignment. In contrast, our method derives multiple alignments from simultaneous superpositions of in- put molecules. Further, our method does not re- quire that all input molecules participate in the alignment. Actually, it efficiently detects high scor- ing partial multiple alignments for all possible num- ber of molecules in the input. To demonstrate the power of MultiProt, we provide a number of case studies. First, we demonstrate known multiple align- ments of protein structures to illustrate the perfor- mance of MultiProt. Next, we present various biologi- cal applications. These include: (1) a partial alignment of hinge-bent domains; (2) identification of functional groups of G-proteins; (3) analysis of binding sites; and (4) protein-protein interface align- ment. Some applications preserve the sequence or- der of the residues in the alignment, whereas others are order-independent. It is their residue sequence order-independence that allows application of MultiProt to derive multiple alignments of binding sites and of protein-protein interfaces, making Mul- tiProt an extremely useful structural tool. Proteins
Another direction in this field was taken by in @cite_25 where they used the . They took 3 atoms or 3 @math -carbon atom triplets (both can be done) from the protein chains. From n atoms, among @math triplets, they take triplets with some restrictions. At this point they have a set of triplets. Then they prepare a hash table with sides of the triangle as keys to the hash table. Then they selectively align atoms of the two chains using the hash table.