scholarly journals Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions

RNA ◽  
2021 ◽  
pp. rna.078685.121
Author(s):  
Francisco Carrascoza ◽  
Maciej Antczak ◽  
Zhichao Miao ◽  
Eric Westhof ◽  
Marta Szachniuk
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
Data Bank ◽  
3D Models ◽  
Its Sequence ◽  
In Silico Prediction ◽  
General Shape ◽  
Stereochemical Quality ◽  
Three Dimensional Models

In silico prediction is a well-established approach to derive a general shape of an RNA molecule based on its sequence or secondary structure. This paper reports an analysis of the stereochemical quality of the RNA three-dimensional models predicted using dedicated computer programs. The stereochemistry of 1,052 RNA 3D structures, including 1,030 models predicted by fully automated and human-guided approaches within 22 RNA-Puzzles challenges and reference structures, is analysed. The evaluation is based on standards of RNA stereochemistry that the Protein Data Bank requires from deposited experimental structures. Deviations from standard bond lengths and angles, planarity or chirality are quantified. A reduction in the number of such deviations should help in the improvement of RNA 3D structure modelling approaches.

scholarly journals Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions

2021 ◽  
Author(s):  
Francisco Carrascoza ◽  
Maciej Antczak ◽  
Zhichao Miao ◽  
Eric Westhof ◽  
Marta Szachniuk
Keyword(s):  
Structure Prediction ◽  
3D Structure ◽  
Three Dimensional ◽  
Data Bank ◽  
3D Models ◽  
In Silico Prediction ◽  
General Shape ◽  
Stereochemical Quality ◽  
Three Dimensional Models

In silico prediction is a well-established approach to derive a general shape of an RNA molecule based on its sequence or secondary structure. This paper reports on the stereochemical quality of the RNA three-dimensional models predicted using dedicated computer programs. The stereochemistry of 1,052 RNA 3D structures, including 1,030 models predicted by fully automated and human-guided approaches within 22 RNA-Puzzles challenges and reference structures, is analysed. The evaluation is based on standards of stereochemistry, established for RNA, that the Protein Data Bank requires from deposited experimental structures. Deviations from standard bond lengths and angles, planarity or chirality are quantified. A reduction in the number of such deviations should help in the improvement of RNA 3D structure prediction accuracy.

scholarly journals Geomatics Techniques for Submerged Heritage: a Mobile App for Tourism

2020 ◽  
Vol 16 ◽  
Keyword(s):  
New Technology ◽  
Three Dimensional ◽  
3D Models ◽  
Mobile App ◽  
Human Errors ◽  
Tourism Sector ◽  
Ancient City ◽  
Three Dimensional Models

The tourism sector is one of the major industries in Italy that has a high impact on local communities in terms of employment and economy. To show the results of a research project highlighting the use of new technology in the tourism sector, the Geomatics Laboratory of the Mediterranea University of Reggio Calabria has developed a mobile application for tourism. The case study is "Calarcheo Park", a nonaccessible underwater archaeological park located in Reggio Calabria, near the remains of the old walls of the ancient city of Reggio Calabria (Reghion, dating back to about the VIII B.C.). The main aim of this paper is to describe the process to relive and re-propose the experience of a real immersion through a journey in virtual reality. Particular attention was given to the research part concerning the simplification processes of the models inserted within an app for tourism sector. The concept app includes scenarios (seabed) and objects (Castle and artefact) obtained from three-dimensional models realized through photogrammetric techniques, therefore "heavy" models in terms of space necessary to store them, recall them and possibly process them. Considering the visualization purpose, and the metric precision needed, the 3d models were reconstructed using a rapid method. To minimize the difficulties during the direct underwater survey carried out by a human operator (e.g. limited time available during the survey, accentuated inaccuracy due to human errors), the operations were carried out using an experimental ROV (Remote Operated Vehicles), widely used to explore underwater environments, equipped with cameras to perform photogrammetric acquisition in a single dive. To enhance the results and quality of the 3d model, a procedure to improve the image quality, and optimizing the processing is also described. This work therefore illustrates the possibilities of using 3D models created by geomatics techniques within virtual environments for apps for tourism purposes

ASSESSING THE QUALITY OF THE HOMOLOGY-MODELED 3D STRUCTURES FROM ELECTROSTATIC STANDPOINT: TEST ON BACTERIAL NUCLEOSIDE MONOPHOSPHATE KINASE FAMILIES

2007 ◽  
Vol 05 (03) ◽  
pp. 693-715 ◽  
Author(s):  
PETRAS KUNDROTAS ◽  
PAULINA GEORGIEVA ◽  
ALEXANDRA SHOSHEVA ◽  
PETYA CHRISTOVA ◽  
EMIL ALEXOV
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
3D Models ◽  
Structural Defects ◽  
Large Protein ◽  
Homologous Proteins ◽  
X Ray ◽  
3D Structures ◽  
Large Sets

In this study, we address the issue of performing meaningful pKa calculations using homology modeled three-dimensional (3D) structures and analyze the possibility of using the calculated pKa values to detect structural defects in the models. For this purpose, the 3D structure of each member of five large protein families of a bacterial nucleoside monophosphate kinases (NMPK) have been modeled by means of homology-based approach. Further, we performed pKa calculations for the each model and for the template X-ray structures. Each bacterial NMPK family used in the study comprised on average 100 members providing a pool of sequences and 3D models large enough for reliable statistical analysis. It was shown that pKa values of titratable groups, which are highly conserved within a family, tend to be conserved among the models too. We demonstrated that homology modeled structures with sequence identity larger than 35% and gap percentile smaller than 10% can be used for meaningful pKa calculations. In addition, it was found that some highly conserved titratable groups either exhibit large pKa fluctuations among the models or have pKa values shifted by several pH units with respect to the pKa calculated for the X-ray structure. We demonstrated that such case usually indicates structural errors associated with the model. Thus, we argue that pKa calculations can be used for assessing the quality of the 3D models by monitoring fluctuations of the pKa values for highly conserved titratable residues within large sets of homologous proteins.

Study the precision of creating 3D structure modeling form terrestrial laser scanner observations

2018 ◽  
Vol 12 (4) ◽  
pp. 303-309
Author(s):  
Zaki M. Zeidan ◽  
Ashraf A. Beshr ◽  
Ashraf G. Shehata
Keyword(s):  
Structural Model ◽  
3D Structure ◽  
Three Dimensional ◽  
Laser Scanner ◽  
Field Tests ◽  
3D Models ◽  
Terrestrial Laser Scanner ◽  
Analysis Of Results ◽  
3D Structure Modeling

Abstract Laser scanner has become widely used nowadays for several applications in civil engineering. An advantage of laser scanner as compared to other geodetic instruments is its capability of collecting hundreds or even thousands of point per second. Terrestrial laser scanner allows acquiring easy and fast complex geometric data from building, machines, objects, etc. Several experimental and field tests are required to investigate the quality and accuracy of scanner points cloud and the 3D geometric models derived from laser scanner. So this paper investigates the precision of creation three dimensional structural model resulted from terrestrial laser scanner observations. The paper also presented the ability to create 3D model by structural faces depending on the plane equation for each face resulted from coordinates of several observed points cover this face using reflector less total station observations. Precision comparison for the quality of 3D models created from laser scanner observations and structure faces is also presented.The results of the practical measurements, calculations and analysis of results are presented.

scholarly journals Unfolding the Genome: The Case Study of P. falciparum

2018 ◽  
Vol 15 (2) ◽  
Author(s):  
Nelle Varoquaux
Keyword(s):  
Genome Organization ◽  
High Throughput Sequencing ◽  
3D Structure ◽  
Three Dimensional ◽  
3D Models ◽  
Contact Maps ◽  
A Genome ◽  
Three Dimensional Models ◽  
Downstream Analysis

Abstract The development of new ways to probe samples for the three-dimensional (3D) structure of DNA paves the way for in depth and systematic analyses of the genome architecture. 3C-like methods coupled with high-throughput sequencing can now assess physical interactions between pairs of loci in a genome-wide fashion, thus enabling the creation of genome-by-genome contact maps. The spreading of such protocols creates many new opportunities for methodological development: how can we infer 3D models from these contact maps? Can such models help us gain insights into biological processes? Several recent studies applied such protocols to P. falciparum (the deadliest of the five human malaria parasites), assessing its genome organization at different moments of its life cycle. With its small genomic size, fairly simple (yet changing) genomic organization during its lifecyle and strong correlation between chromatin folding and gene expression, this parasite is the ideal case study for applying and developing methods to infer 3D models and use them for downstream analysis. Here, I review a set of methods used to build and analyse three-dimensional models from contact maps data with a special highlight on P. falciparum’s genome organization.

scholarly journals Comparative Analysis of Digital Models of Objects of Cultural Heritage Obtained by the “3D SLS” and “SfM” Methods

2021 ◽  
Vol 11 (12) ◽  
pp. 5321
Author(s):  
Marcin Barszcz ◽  
Jerzy Montusiewicz ◽  
Magdalena Paśnikowska-Łukaszuk ◽  
Anna Sałamacha
Keyword(s):  
Cultural Heritage ◽  
Low Cost ◽  
Three Dimensional ◽  
3D Models ◽  
Silk Road ◽  
Digital Models ◽  
Global Pandemic ◽  
University Of Technology ◽  
Three Dimensional Models ◽  
3D Digitisation

In the era of the global pandemic caused by the COVID-19 virus, 3D digitisation of selected museum artefacts is becoming more and more frequent practice, but the vast majority is performed by specialised teams. The paper presents the results of comparative studies of 3D digital models of the same museum artefacts from the Silk Road area generated by two completely different technologies: Structure from Motion (SfM)—a method belonging to the so-called low-cost technologies—and by Structured-light 3D Scanning (3D SLS). Moreover, procedural differences in data acquisition and their processing to generate three-dimensional models are presented. Models built using a point cloud were created from data collected in the Afrasiyab museum in Samarkand (Uzbekistan) during “The 1st Scientific Expedition of the Lublin University of Technology to Central Asia” in 2017. Photos for creating 3D models in SfM technology were taken during a virtual expedition carried out under the “3D Digital Silk Road” program in 2021. The obtained results show that the quality of the 3D models generated with SfM differs from the models from the technology (3D SLS), but they may be placed in the galleries of the vitrual museum. The obtained models from SfM do not have information about their size, which means that they are not fully suitable for archiving purposes of cultural heritage, unlike the models from SLS.

scholarly journals Improving 3D-3D facial registration methods: potential role of three-dimensional models in personal identification of the living

2021 ◽  
Author(s):  
Daniele Gibelli ◽  
Andrea Palamenghi ◽  
Pasquale Poppa ◽  
Chiarella Sforza ◽  
Cristina Cattaneo ◽  
...  
Keyword(s):  
Three Dimensional ◽  
3D Models ◽  
Personal Identification ◽  
Surveillance Systems ◽  
3D Registration ◽  
Three Dimensional Models ◽  
Point To Point ◽  
Point Distance ◽  
Male Subjects

AbstractPersonal identification of the living from video surveillance systems usually involves 2D images. However, the potentiality of three-dimensional facial models in gaining personal identification through 3D-3D comparison still needs to be verified. This study aims at testing the reliability of a protocol for 3D-3D registration of facial models, potentially useful for personal identification. Fifty male subjects aged between 18 and 45 years were randomly chosen from a database of 3D facial models acquired through stereophotogrammetry. For each subject, two acquisitions were available; the 3D models of faces were then registered onto other models belonging to the same and different individuals according to the least point-to-point distance on the entire facial surface, for a total of 50 matches and 50 mismatches. RMS value (root mean square) of point-to-point distance between the two models was then calculated through the VAM® software. Intra- and inter-observer errors were assessed through calculation of relative technical error of measurement (rTEM). Possible statistically significant differences between matches and mismatches were assessed through Mann–Whitney test (p < 0.05). Both for intra- and inter-observer repeatability rTEM was between 2.2 and 5.2%. Average RMS point-to-point distance was 0.50 ± 0.28 mm in matches, 2.62 ± 0.56 mm in mismatches (p < 0.01). An RMS threshold of 1.50 mm could distinguish matches and mismatches in 100% of cases. This study provides an improvement to existing 3D-3D superimposition methods and confirms the great advantages which may derive to personal identification of the living from 3D facial analysis.

scholarly journals Creation of virtual 3D models of the existing architectonic structures using the web resources

Spatium ◽  
2016 ◽  
pp. 30-36 ◽  
Author(s):  
Petar Pejic ◽  
Sonja Krasic
Keyword(s):  
Laser Scanning ◽  
Three Dimensional ◽  
3D Models ◽  
Three Dimensional Model ◽  
Web Resources ◽  
Existing Structures ◽  
Software Packages ◽  
Physical Presence ◽  
The Creation ◽  
Three Dimensional Models

Digital three-dimensional models of the existing architectonic structures are created for the purpose of digitalization of the archive documents, presentation of buildings or an urban entity or for conducting various analyses and tests. Traditional methods for the creation of 3D models of the existing buildings assume manual measuring of their dimensions, using the photogrammetry method or laser scanning. Such approaches require considerable time spent in data acquisition or application of specific instruments and equipment. The goal of this paper is presentation of the procedure for the creation of 3D models of the existing structures using the globally available web resources and free software packages on standard PCs. This shortens the time of the production of a digital three-dimensional model of the structure considerably and excludes the physical presence at the location. In addition, precision of this method was tested and compared with the results acquired in a previous research.

scholarly journals Processing Three-Dimensional Models of Archaeological Artifacts

2021 ◽  
Vol 20 (7) ◽  
pp. 48-61
Author(s):  
Pavel V. Chistyakov ◽  
Ekaterina N. Bocharova ◽  
Ksenia A. Kolobova
Keyword(s):  
Three Dimensional ◽  
3D Models ◽  
International Standards ◽  
Post Processing ◽  
Three Dimensional Model ◽  
Scaled Model ◽  
Three Dimensional Modeling ◽  
Dimensional Modeling ◽  
Dimensional Models ◽  
Three Dimensional Models

This article provides a detailed account of the process of scanning, post-processing and further manipulation of three-dimensional models obtained with structured light scanners. Purpose. The purpose of the study is determined by the need for national archaeologists to learn the methods of three-dimensional modeling for the implementation of scientific research corresponding to international standards. Unfortunately, this direction in national archaeology began to develop in a relatively recent time and there is a lag in the application of three-dimensional modeling of national archaeology compared to the world level. Results. Any archaeological, experimental or ethnographic artifact can be used for three-dimensional scanning. To perform post-processing of three-dimensional models it is necessary to carry out primary scanning of an artifact by one of the existing algorithms. The algorithm for creating models, their positioning, simplification, saving in various formats and export is described. The main sequence of 3D models post-processing includes: processing of groups of scanned projections (their cleaning and alignment), creation of artifact model and processing/rectification of the resulting model using special software. Conclusion. As a result of correct implementation of the algorithm, the researcher receives a scaled model completely corresponding to the original artifact. Obtaining a scalable, texture-free three-dimensional model of the artifact, which fully corresponds to the original and exceeds a photograph in the quality of detail transfer, allows a scientist to conduct precise metric measurements and any procedures of non-invasive manipulation of the models. The ability to access a database of three-dimensional models of archaeological collections greatly simplifies the work of archaeologists, especially in situations when country borders are closed.

Online quality evaluation of tissue paper structure on new generation tissue machines

2018 ◽  
Vol 33 (1) ◽  
pp. 133-141 ◽  
Author(s):  
Jukka-Pekka Raunio ◽  
Tommi Löyttyniemi ◽  
Risto Ritala
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
Surface Profile ◽  
Absorption Capacity ◽  
Tissue Paper ◽  
Paper Manufacturing ◽  
Residual Variation ◽  
Residual Variances ◽  
New Generation

Abstract At present, the tissue paper manufacturing is mostly based on the dry crepe technology. During the last decade, the manufacturers have introduced new tissue machines concepts that increase the softness, bulk, and absorption capacity. Such machines produce a strong regular three-dimensional (3D) structure to the sheet before the Yankee cylinder. At present, the quality of the 3D structure is not evaluated, or it is evaluated only subjectively at the mill. This is mostly because of the difficulties to separate reliably the regular 3D pattern from other variations. This paper introduces a frequency analysis based method which separates the surface profile variances in tissue paper to the creping, to the regular 3D pattern and to the residual variation. The 3D surface profiles and their variances were determined online with the photometric stereo method. We show that the introduced analysis method evaluates the variance portions reliably and the results are consistent with the visual perception of the 3D surfaces. In one particular product, the regular 3D pattern explains 74 % of total surface variance; the creping explains 10 % and residual variations 16 %. Furthermore, the creping and residual variances are quite stable over time whereas the variance of the regular 3D pattern fluctuates significantly.

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