42,430 research outputs found

    Spherical harmonics coeffcients for ligand-based virtual screening of cyclooxygenase inhibitors

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    Background: Molecular descriptors are essential for many applications in computational chemistry, such as ligand-based similarity searching. Spherical harmonics have previously been suggested as comprehensive descriptors of molecular structure and properties. We investigate a spherical harmonics descriptor for shape-based virtual screening. Methodology/Principal Findings: We introduce and validate a partially rotation-invariant three-dimensional molecular shape descriptor based on the norm of spherical harmonics expansion coefficients. Using this molecular representation, we parameterize molecular surfaces, i.e., isosurfaces of spatial molecular property distributions. We validate the shape descriptor in a comprehensive retrospective virtual screening experiment. In a prospective study, we virtually screen a large compound library for cyclooxygenase inhibitors, using a self-organizing map as a pre-filter and the shape descriptor for candidate prioritization. Conclusions/Significance: 12 compounds were tested in vitro for direct enzyme inhibition and in a whole blood assay. Active compounds containing a triazole scaffold were identified as direct cyclooxygenase-1 inhibitors. This outcome corroborates the usefulness of spherical harmonics for representation of molecular shape in virtual screening of large compound collections. The combination of pharmacophore and shape-based filtering of screening candidates proved to be a straightforward approach to finding novel bioactive chemotypes with minimal experimental effort

    Chemoinformatics Research at the University of Sheffield: A History and Citation Analysis

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    This paper reviews the work of the Chemoinformatics Research Group in the Department of Information Studies at the University of Sheffield, focusing particularly on the work carried out in the period 1985-2002. Four major research areas are discussed, these involving the development of methods for: substructure searching in databases of three-dimensional structures, including both rigid and flexible molecules; the representation and searching of the Markush structures that occur in chemical patents; similarity searching in databases of both two-dimensional and three-dimensional structures; and compound selection and the design of combinatorial libraries. An analysis of citations to 321 publications from the Group shows that it attracted a total of 3725 residual citations during the period 1980-2002. These citations appeared in 411 different journals, and involved 910 different citing organizations from 54 different countries, thus demonstrating the widespread impact of the Group's work

    Segmentation and semantic labelling of RGBD data with convolutional neural networks and surface fitting

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    We present an approach for segmentation and semantic labelling of RGBD data exploiting together geometrical cues and deep learning techniques. An initial over-segmentation is performed using spectral clustering and a set of non-uniform rational B-spline surfaces is fitted on the extracted segments. Then a convolutional neural network (CNN) receives in input colour and geometry data together with surface fitting parameters. The network is made of nine convolutional stages followed by a softmax classifier and produces a vector of descriptors for each sample. In the next step, an iterative merging algorithm recombines the output of the over-segmentation into larger regions matching the various elements of the scene. The couples of adjacent segments with higher similarity according to the CNN features are candidate to be merged and the surface fitting accuracy is used to detect which couples of segments belong to the same surface. Finally, a set of labelled segments is obtained by combining the segmentation output with the descriptors from the CNN. Experimental results show how the proposed approach outperforms state-of-the-art methods and provides an accurate segmentation and labelling

    Asymmetric Feature Maps with Application to Sketch Based Retrieval

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    We propose a novel concept of asymmetric feature maps (AFM), which allows to evaluate multiple kernels between a query and database entries without increasing the memory requirements. To demonstrate the advantages of the AFM method, we derive a short vector image representation that, due to asymmetric feature maps, supports efficient scale and translation invariant sketch-based image retrieval. Unlike most of the short-code based retrieval systems, the proposed method provides the query localization in the retrieved image. The efficiency of the search is boosted by approximating a 2D translation search via trigonometric polynomial of scores by 1D projections. The projections are a special case of AFM. An order of magnitude speed-up is achieved compared to traditional trigonometric polynomials. The results are boosted by an image-based average query expansion, exceeding significantly the state of the art on standard benchmarks.Comment: CVPR 201

    Reference face graph for face recognition

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    Face recognition has been studied extensively; however, real-world face recognition still remains a challenging task. The demand for unconstrained practical face recognition is rising with the explosion of online multimedia such as social networks, and video surveillance footage where face analysis is of significant importance. In this paper, we approach face recognition in the context of graph theory. We recognize an unknown face using an external reference face graph (RFG). An RFG is generated and recognition of a given face is achieved by comparing it to the faces in the constructed RFG. Centrality measures are utilized to identify distinctive faces in the reference face graph. The proposed RFG-based face recognition algorithm is robust to the changes in pose and it is also alignment free. The RFG recognition is used in conjunction with DCT locality sensitive hashing for efficient retrieval to ensure scalability. Experiments are conducted on several publicly available databases and the results show that the proposed approach outperforms the state-of-the-art methods without any preprocessing necessities such as face alignment. Due to the richness in the reference set construction, the proposed method can also handle illumination and expression variation
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