1.1CVOct 4, 2016
A novel and effective scoring scheme for structure classification and pairwise similarity measurementRezaul Karim, Md. Momin Al Aziz, Swakkhar Shatabda et al.
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 http://research.buet.ac.bd:8080/Comograd/score.html where you can get the similarity measurement score between two protein structures based on our method.
CoMOGrad and PHOG: From Computer Vision to Fast and Accurate Protein Tertiary Structure RetrievalRezaul Karim, Mohd. Momin Al Aziz, Swakkhar Shatabda et al.
Due to the advancements in technology number of entries in the structural database of proteins are increasing day by day. Methods for retrieving protein tertiary structures from this large database is the key to comparative analysis of structures which plays an important role to understand proteins and their function. In this paper, we present fast and accurate methods for the retrieval of proteins from a large database with tertiary structures similar to a query protein. Our proposed methods borrow ideas from the field of computer vision. The speed and accuracy of our methods comes from the two newly introduced features, the co-occurrence matrix of the oriented gradient and pyramid histogram of oriented gradient and from the use of Euclidean distance as the distance measure. Experimental results clearly indicate the superiority of our approach in both running time and accuracy. Our method is readily available for use from this website: http://research.buet.ac.bd:8080/Comograd/.