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.
ProteinDBS @cite_16 is another method that uses some common features of CBIR (Content Based Image Retrieval) to compare @math -carbon distance matrix images. This method is much faster than the previous ones as it compares only some specific image features. Notably however, the feature preprocessing done by ProteinDBS is computationally expensive.
@cite_16
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We have developed a web server (ProteinDBS) for the life science community to search for similar protein tertiary structures in real time. This system applies computer visualization techniques to extract the predominant visual patterns encoded in two-dimensional distance matrices generated from the three-dimensional coordinates of protein chains. When meaningful contents, represented in a multi-dimensional feature space, have been extracted from distance matrices, an advanced indexing structure, Entropy Balanced Statistical (EBS) k-d tree, is utilized to index the data. Our system is able to return search results in ranked order from a database with 46075 chains in seconds, exhibiting a reasonably high degree of precision. To our knowledge, this is the first real-time search engine for protein structure comparison. ProteinDBS provides two types of query method: query by Protein Data Bank protein chain ID and by new structures uploaded by users. The system is hosted at http: ProteinDBS.rnet.missouri.edu. Local descriptors are mostly extracted over the raw intensity values of the image and requires the analysis of patterns in local pixel neighborhoods. The raw images don't provide much local relationship information required for the local descriptors. To resolve this problem, a new method of local image feature description is proposed in this paper based on the patterns extracted from the multiple filtered images. The whole process is structured as follows: First, the images are filtered with the bag of filters (BoF) and then local binary pattern (LBP) is computed over each filtered image and finally concatenated to find out the single BoF-LBP descriptor. The local information enriches in the filtered images improves the discriminative ability of the final descriptor. Content based image retrieval (CBIR) experiments are performed to observe the effectiveness of the proposed approach and compared with the recent state-of-the-art methods. The experiments are conducted over four benchmark databases having natural and texture images such as Corel-1k, Corel-10k, MIT-VisTex and STex-512S. The experimental results confirm that the introduced approach is able to improve the retrieval performance of the CBIR system. Given the growing amount of very large image databases, content based image retrieval (CBIR) is becoming more and more important. One of the major challenges in CBIR is the semantic gap - commonly used feature-based algorithms are not able to identify what really draws human attention in an image. This problem is more crucial for localized CBIR, where certain regions parts of the image are what the user is really interested in. This paper explores how human gaze can be utilized to extract regions of interest (ROIs) of an image to perform attention based image retrieval. Using eye tracking data and knowledge about foveal and peripheral vision of humans, we present a foveal fixation clustering algorithm that automatically generates ROIs in an image while a person is viewing it. To objectively set different parameters of the algorithm, a small user study was conducted. The method was evaluated for use in a localized CBIR system. Image retrieval results using the publicly available SIVAL dataset were scored using mean average precision (MAP). Comparison to a saliency-based visual attention algorithm as well as to manually labeled regions showed that the retrieval results of the developed algorithm are nearly two times better than the saliency-based visual attention algorithm and very close to the results using hand-labeled regions. In Content-based Image Retrieval (CBIR) systems, ranking accurately collection images is of great relevance. Users are interested in the returned images placed at the first positions, which usually are the most relevant ones. Collection images are ranked in increasing order of their distance to the query pattern (e.g., query image) defined by users. Therefore, the effectiveness of these systems is very dependent on the accuracy of the distance function adopted. In this paper, we present a novel context-based approach for redefining distances and later re-ranking images aiming to improve the effectiveness of CBIR systems. In our approach, distances among images are redefined based on the similarity of their ranked lists. Conducted experiments involving shape, color, and texture descriptors demonstrate the effectiveness of our method.