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.
CE or method @cite_7 is similar to DALI in that it too breaks each structure in the query set into a series of fragments that it then attempts to reassemble into a complete alignment. A series of pairwise combinations of fragments called aligned fragment pairs, or AFPs, are used to define a similarity matrix through which an optimal path is generated to identify the final alignment. Only AFPs that meet given criteria for local similarity are included in the matrix as a means of reducing the necessary search space and thereby increasing efficiency @cite_7 . However, in spite of having good accuracy it is impossible to implement these two methods as a real time web service due to their huge computational cost.
@cite_7
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A new algorithm is reported which builds an alignment between two protein structures. The algorithm involves a combinatorial extension (CE) of an alignment path defined by aligned fragment pairs (AFPs) rather than the more conventional techniques using dynamic programming and Monte Carlo optimization. AFPs, as the name suggests, are pairs of fragments, one from each protein, which confer structure similarity. AFPs are based on local geometry, rather than global features such as orientation of secondary structures and overall topology. Combinations of AFPs that represent possible continuous alignment paths are selectively extended or discarded thereby leading to a single optimal alignment. The algorithm is fast and accurate in finding an optimal structure alignment and hence suitable for database scanning and detailed analysis of large protein families. The method has been tested and compared with results from Dali and VAST using a representative sample of similar structures. Several new structural similarities not detected by these other methods are reported. Specific one-on-one alignments and searches against all structures as found in the Protein Data Bank (PDB) can be performed via the Web at http: cl.sdsc.edu ce.html. We introduce 4PCS, a fast and robust alignment scheme for 3D point sets that uses wide bases, which are known to be resilient to noise and outliers. The algorithm allows registering raw noisy data, possibly contaminated with outliers, without pre-filtering or denoising the data. Further, the method significantly reduces the number of trials required to establish a reliable registration between the underlying surfaces in the presence of noise, without any assumptions about starting alignment. Our method is based on a novel technique to extract all coplanar 4-points sets from a 3D point set that are approximately congruent, under rigid transformation, to a given set of coplanar 4-points. This extraction procedure runs in roughly O(n2 + k) time, where n is the number of candidate points and k is the number of reported 4-points sets. In practice, when noise level is low and there is sufficient overlap, using local descriptors the time complexity reduces to O(n + k). We also propose an extension to handle similarity and affine transforms. Our technique achieves an order of magnitude asymptotic acceleration compared to common randomized alignment techniques. We demonstrate the robustness of our algorithm on several sets of multiple range scans with varying degree of noise, outliers, and extent of overlap. We introduce a co-analysis technique designed for correspondence inference within large shape collections. Such collections are naturally rich in variation, adding ambiguity to the notoriously difficult problem of correspondence computation. We leverage the robustness of correspondences between similar shapes to address the difficulties associated with this problem. In our approach, pairs of similar shapes are extracted from the collection, analyzed and matched in an efficient and reliable manner, culminating in the construction of a network of correspondences that connects the entire collection. The correspondence between any pair of shapes then amounts to a simple propagation along the minimax path between the two shapes in the network. At the heart of our approach is the introduction of a robust, structure-oriented shape matching method. Leveraging the idea of projective analysis, we partition 2D projections of a shape to obtain a set of 1D ordered regions, which are both simple and efficient to match. We lift the matched projections back to the 3D domain to obtain a pairwise shape correspondence. The emphasis given to structural compatibility is a central tool in estimating the reliability and completeness of a computed correspondence, uncovering any non-negligible semantic discrepancies that may exist between shapes. These detected differences are a deciding factor in the establishment of a network aiming to capture local similarities. We demonstrate that the combination of the presented observations into a co-analysis method allows us to establish reliable correspondences among shapes within large collections. This paper presents a method for pairwise 3D alignment which solves data association by matching scan segments across scans. Generating accurate segment associations allows to run a modified version of the Iterative Closest Point (ICP) algorithm where the search for point-to-point correspondences is constrained to associated segments. The novelty of the proposed approach is in the segment matching process which takes into account the proximity of segments, their shape, and the consistency of their relative locations in each scan. Scan segmentation is here assumed to be given (recent studies provide various alternatives [10], [19]). The method is tested on seven sequences of Velodyne scans acquired in urban environments. Unlike various other standard versions of ICP, which fail to recover correct alignment when the displacement between scans increases, the proposed method is shown to be robust to displacements of several meters. In addition, it is shown to lead to savings in computational times which are potentially critical in real-time applications.