Search results for " Computer-Aided design"
showing 10 items of 232 documents
Rocker: Open source, easy-to-use tool for AUC and enrichment calculations and ROC visualization
2016
Receiver operating characteristics (ROC) curve with the calculation of area under curve (AUC) is a useful tool to evaluate the performance of biomedical and chemoinformatics data. For example, in virtual drug screening ROC curves are very often used to visualize the efficiency of the used application to separate active ligands from inactive molecules. Unfortunately, most of the available tools for ROC analysis are implemented into commercially available software packages, or are plugins in statistical software, which are not always the easiest to use. Here, we present Rocker, a simple ROC curve visualization tool that can be used for the generation of publication quality images. Rocker also…
Conf-VLKA: A structure-based revisitation of the Virtual Lock-and-key Approach
2016
In a previous work, we developed the in house Virtual Lock-and-Key Approach (VLKA) in order to evaluate target assignment starting from molecular descriptors calculated on known inhibitors used as an information source. This protocol was able to predict the correct biological target for the whole dataset with a good degree of reliability (80%), and proved experimentally, which was useful for the target fishing of unknown compounds. In this paper, we tried to remodel the previous in house developed VLKA in a more sophisticated one in order to evaluate the influence of 3D conformation of ligands on the accuracy of the prediction. We applied the same previous algorithm of scoring and ranking b…
Identification of estrogen receptor α ligands with virtual screening techniques.
2016
Utilization of computer-aided molecular discovery methods in virtual screening (VS) is a cost-effective approach to identify novel bioactive small molecules. Unfortunately, no universal VS strategy can guarantee high hit rates for all biological targets, but each target requires distinct, fine-tuned solutions. Here, we have studied in retrospective manner the effectiveness and usefulness of common pharmacophore hypothesis, molecular docking and negative image-based screening as potential VS tools for a widely applied drug discovery target, estrogen receptor α (ERα). The comparison of the methods helps to demonstrate the differences in their ability to identify active molecules. For example,…
QuBiLS-MAS, open source multi-platform software for atom- and bond-based topological (2D) and chiral (2.5D) algebraic molecular descriptors computati…
2017
Background In previous reports, Marrero-Ponce et al. proposed algebraic formalisms for characterizing topological (2D) and chiral (2.5D) molecular features through atom- and bond-based ToMoCoMD-CARDD (acronym for Topological Molecular Computational Design-Computer Aided Rational Drug Design) molecular descriptors. These MDs codify molecular information based on the bilinear, quadratic and linear algebraic forms and the graph-theoretical electronic-density and edge-adjacency matrices in order to consider atom- and bond-based relations, respectively. These MDs have been successfully applied in the screening of chemical compounds of different therapeutic applications ranging from antimalarials…
An Efficient Cooperative Smearing Technique for Degraded Historical Documents Images Segmentation
2020
Segmentation is one of the critical steps in historical document image analysis systems that determines the quality of the search, understanding, recognition and interpretation processes. It allows isolating the objects to be considered and separating the regions of interest (paragraphs, lines, words and characters) from other entities (figures, graphs, tables, etc.). This stage follows the thresholding, which aims to improve the quality of the document and to extract its background from its foreground, also for detecting and correcting the skew that leads to redress the document. Here, a hybrid method is proposed in order to locate words and characters in both handwritten and printed docu…
Accurate estimation of retinal vessel width using bagged decision trees and an extended multiresolution Hermite model.
2012
We present an algorithm estimating the width of retinal vessels in fundus camera images. The algorithm uses a novel parametric surface model of the cross-sectional intensities of vessels, and ensembles of bagged decision trees to estimate the local width from the parameters of the best-fit surface. We report comparative tests with REVIEW, currently the public database of reference for retinal width estimation, containing 16 images with 193 annotated vessel segments and 5066 profile points annotated manually by three independent experts. Comparative tests are reported also with our own set of 378 vessel widths selected sparsely in 38 images from the Tayside Scotland diabetic retinopathy scre…
Using Augmented Reality to Treat Phobias
2005
Virtual reality (VR) is useful for treating several psychological problems, including phobias such as fear of flying, agoraphobia, claustrophobia, and phobia to insects and small animals. We believe that augmented reality (AR) could also be used to treat some psychological disorders. AR and VR share some advantages over traditional treatments. However, AR gives a greater feeling of presence (the sensation of being there) and reality judgment (judging an experience as real) than VR because the environment and the elements the patient uses to interact with the application are real. Moreover, in AR users see their own hands, feet, and so on, whereas VR only simulates this experience. With thes…
Skull Bone Defects Reconstruction with Custom-Made Titanium Graft shaped with Electron Beam Melting Technology: Preliminary Experience in a Series of…
2017
Background: Cranioplasty represents a challenge in neurosurgery. Its goal is not only plastic reconstruction of the skull but also to restore and preserve cranial function, to improve cerebral hemodynamics, and to provide mechanical protection of the neural structures. The ideal material for the reconstructive procedures and the surgical timing are still controversial. Many alloplastic materials are available for performing cranioplasty and among these, titanium still represents a widely proven and accepted choice. Methods: The aim of our study was to present our preliminary experience with a “custom-made” cranioplasty, using electron beam melting (EBM) technology, in a series of ten patien…
Digital Mosaic Frameworks - an overview
2007
Art often provides valuable hints for technological innovations especially in the field of Image Processing and Computer Graphics. In this paper we survey in a unified framework several methods to transform raster input images into good quality mosaics. For each of the major different approaches in literature the paper reports a short description and a discussion of the most relevant issues. To complete the survey comparisons among the different techniques both in terms of visual quality and computational complexity are provided.
LogDet divergence-based metric learning with triplet constraints and its applications.
2014
How to select and weigh features has always been a difficult problem in many image processing and pattern recognition applications. A data-dependent distance measure can address this problem to a certain extent, and therefore an accurate and efficient metric learning becomes necessary. In this paper, we propose a LogDet divergence-based metric learning with triplet constraints (LDMLT) approach, which can learn Mahalanobis distance metric accurately and efficiently. First of all, we demonstrate the good properties of triplet constraints and apply it in LogDet divergence-based metric learning model. Then, to deal with high-dimensional data, we apply a compressed representation method to learn…