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

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

Improving 3D Shape Retrieval Methods based on Bag-of-Feature Approach by using Local Codebooks

Also available online at http://www.sersc.org/journals/IJFGCN/vol5_no4/3.pdfInternational audienceRecent investigations illustrate that view-based methods, with pose normalization pre-processing get better performances in retrieving rigid models than other approaches and still the most popular and practical methods in the field of 3D shape retrieval. In this paper we present an improvement of 3D shape retrieval methods based on bag-of features approach. These methods use this approach to integrate a set of features extracted from 2D views of the 3D objects using the SIFT (Scale Invariant Feature Transform) algorithm into histograms using vector quantization which is based on a global visual codebook. In order to improve the retrieval performances, we propose to associate to each 3D object its local visual codebook instead of a unique global codebook. The experimental results obtained on the Princeton Shape Benchmark database, for the BF-SIFT method proposed by Ohbuchi, et al., and CM-BOF proposed by Zhouhui, et al., show that the proposed approach performs better than the original approach

A predictive approach for a real-time remote visualization of large meshes

Déjà sur HALRemote access to large meshes is the subject of studies since several years. We propose in this paper a contribution to the problem of remote mesh viewing. We work on triangular meshes. After a study of existing methods of remote viewing, we propose a visualization approach based on a client-server architecture, in which almost all operations are performed on the server. Our approach includes three main steps: a first step of partitioning the original mesh, generating several fragments of the original mesh that can be supported by the supposed smaller Transfer Control Protocol (TCP) window size of the network, a second step called pre-simplification of the mesh partitioned, generating simplified models of fragments at different levels of detail, which aims to accelerate the visualization process when a client(that we also call remote user) requests a visualization of a specific area of interest, the final step involves the actual visualization of an area which interest the client, the latter having the possibility to visualize more accurately the area of interest, and less accurately the areas out of context. In this step, the reconstruction of the object taking into account the connectivity of fragments before simplifying a fragment is necessary.Pestiv-3D projec

Enhanced 2D/3D Approaches Based on Relevance Index for 3D-Shape Retrieval

International audienceWe present a new approach for 3D model indexing and retrieval using 2D/3D shape descriptors based on silhouettes or depth-buffer images. To take into account the dispersion of information in the views, we associate to each view a relevance index which will be afterward used in the dissimilarity computation. The performance of this new approach is evaluated on the Princeton 3D Shape Benchmark database

Spherical Harmonics Coefficients for Ligand-Based Virtual Screening of Cyclooxygenase Inhibitors

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.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.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

The Evolution of First Person Vision Methods: A Survey

The emergence of new wearable technologies such as action cameras and smart-glasses has increased the interest of computer vision scientists in the First Person perspective. Nowadays, this field is attracting attention and investments of companies aiming to develop commercial devices with First Person Vision recording capabilities. Due to this interest, an increasing demand of methods to process these videos, possibly in real-time, is expected. Current approaches present a particular combinations of different image features and quantitative methods to accomplish specific objectives like object detection, activity recognition, user machine interaction and so on. This paper summarizes the evolution of the state of the art in First Person Vision video analysis between 1997 and 2014, highlighting, among others, most commonly used features, methods, challenges and opportunities within the field.Comment: First Person Vision, Egocentric Vision, Wearable Devices, Smart Glasses, Computer Vision, Video Analytics, Human-machine Interactio

An overview of view-based 2D-3D indexing methods

International audienceThis paper proposes a comprehensive overview of state of the art 2D/3D, view-based indexing methods. The principle of 2D/3D indexing methods consists of describing 3D models by means of a set of 2D shape descriptors, associated with a set of corresponding 2D views (under the assumption of a given projection model). Notably, such an approach makes it possible to identify 3D objects of interest from 2D images/videos. An experimental evaluation is also proposed, in order to examine the influence of the number of views and of the associated viewing angle selection strategies on the retrieval results. Experiments concern both 3D model retrieval and image recognition from a single view. Results obtained show promising performances, with recognition rates from a single view higher then 66%, which opens interesting perspectives in terms of semantic metadata extraction from still images/videos

State of the Art on Stylized Fabrication

© 2018 The Authors Computer Graphics Forum © 2018 The Eurographics Association and John Wiley & Sons Ltd. Digital fabrication devices are powerful tools for creating tangible reproductions of 3D digital models. Most available printing technologies aim at producing an accurate copy of a tridimensional shape. However, fabrication technologies can also be used to create a stylistic representation of a digital shape. We refer to this class of methods as ‘stylized fabrication methods’. These methods abstract geometric and physical features of a given shape to create an unconventional representation, to produce an optical illusion or to devise a particular interaction with the fabricated model. In this state-of-the-art report, we classify and overview this broad and emerging class of approaches and also propose possible directions for future research