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 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.

Is the growth rate of Protein Data Bank sufficient to solve the protein structure prediction problem using template-based modeling?

2015 ◽  
Vol 11 (1) ◽  
pp. 1-7 ◽  
Author(s):  
Michal Brylinski
Keyword(s):  
Protein Structure ◽  
Protein Data Bank ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Structural Information ◽  
Three Dimensional ◽  
Data Bank ◽  
Prediction Problem ◽  
Three Dimensional Models ◽  
Protein Structure Prediction Problem

AbstractThe Protein Data Bank (PDB) undergoes an exponential expansion in terms of the number of macromolecular structures deposited every year. A pivotal question is how this rapid growth of structural information improves the quality of three-dimensional models constructed by contemporary bioinformatics approaches. To address this problem, we performed a retrospective analysis of the structural coverage of a representative set of proteins using remote homology detected by COMPASS and HHpred. We show that the number of proteins whose structures can be confidently predicted increased during a 9-year period between 2005 and 2014 on account of the PDB growth alone. Nevertheless, this encouraging trend slowed down noticeably around the year 2008 and has yielded insignificant improvements ever since. At the current pace, it is unlikely that the protein structure prediction problem will be solved in the near future using existing template-based modeling techniques. Therefore, further advances in experimental structure determination, qualitatively better approaches in fold recognition, and more accurate template-free structure prediction methods are desperately needed.

scholarly journals REALDIST: Real-valued protein distance prediction

2020 ◽  
Author(s):  
Badri Adhikari
Keyword(s):  
Structure Prediction ◽  
3D Structure ◽  
Three Dimensional ◽  
Prediction Method ◽  
3D Models ◽  
Classification Problem ◽  
Intermediate Step ◽  
Protein Distance ◽  
Multi Class Classification ◽  
Distance Prediction

AbstractProtein structure prediction continues to stand as an unsolved problem in bioinformatics and biomedicine. Deep learning algorithms and the availability of metagenomic sequences have led to the development of new approaches to predict inter-residue distances—the key intermediate step. Different from the recently successful methods which frame the problem as a multi-class classification problem, this article introduces a real-valued distance prediction method REALDIST. Using a representative set of 43 thousand protein chains, a variant of deep ResNet is trained to predict real-valued distance maps. The contacts derived from the real-valued distance maps predicted by this method, on the most difficult CASP13 free-modeling protein datasets, demonstrate a long-range top-L precision of 52%, which is 17% higher than the top CASP13 predictor Raptor-X and slightly higher than the more recent trRosetta method. Similar improvements are observed on the CAMEO ‘hard’ and ‘very hard’ datasets. Three-dimensional (3D) structure prediction guided by real-valued distances reveals that for short proteins the mean accuracy of the 3D models is slightly higher than the top human predictor AlphaFold and server predictor Quark in the CASP13 competition.

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 Structure prediction of the druggable fragments in SARS-CoV-2 untranslated regions

2021 ◽  
Author(s):  
Julita Gumna ◽  
Maciej Antczak ◽  
Ryszard Walenty Adamiak ◽  
Janusz Marek Bujnicki ◽  
Shi-Jie Chen ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Structure Prediction ◽  
3D Structure ◽  
Three Dimensional ◽  
3D Models ◽  
Untranslated Regions ◽  
Dimensional Structure ◽  
Consensus Structure ◽  
Computational Tools ◽  
Functional Regions

The outbreak of the COVID-19 pandemic has led to intensive studies of both the structure and replication mechanism of SARS-CoV-2. In spite of some secondary structure experiments being carried out, the 3D structure of the key functional regions of the viral RNA has not yet been well understood. At the beginning of COVID-19 breakout, the RNA-Puzzles community attempted to envisage the three-dimensional structure of 5′- and 3′-Un-Translated Regions (UTRs) of the SARS-CoV-2 genome. Here, we report the results of this prediction challenge, presenting the methodologies developed by six participating groups and discussing 100 RNA 3D models (60 models of 5′-UTR and 40 of 3′-UTR) predicted through applying both human experts and automated server approaches. We describe the original protocol for the reference-free comparative analysis of RNA 3D structures designed especially for this challenge. We elaborate on the deduced consensus structure and the reliability of the predicted structural motifs. All the computationally simulated models, as well as the development and the testing of computational tools dedicated to 3D structure analysis, are available for further study.

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.

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