3D Structural Bioinformatics of Proteins and Antibodies: State of the Art Perspectives and Challenges

2013 ◽  
Vol 2 (3) ◽  
pp. 67-74
Author(s):  
Arianna Filntisi ◽  
Dimitrios Vlachakis ◽  
George Matsopoulos ◽  
Sophia Kossida
Keyword(s):  
Quantum Mechanics ◽  
Quantum Chemical ◽  
State Of The Art ◽  
Three Dimensional ◽  
Research Field ◽  
Important Class ◽  
Structural Components ◽  
Molecular Systems ◽  
Mechanical Methods ◽  
Harmful Substances

Proteins are an important class of biochemical molecules, as the structural components of animal and human tissue are based on them. Antibodies are proteins that play a crucial role in the preservation of life since they are produced by the body's immune system as a response to harmful substances. The modelling of proteins and antibodies in particular is a vibrant research field which facilitates the design of drugs, a process otherwise demanding in terms of time and resources. A variety of computational methods and tools are being developed towards that goal, among which are hybrid quantum chemical/molecular mechanical methods and three-dimensional antibody modelling. In this review the authors discuss the knowledge concerning proteins and antibodies, as well as the use of quantum mechanics in the simulation of molecular systems and the three-dimensional antibody modelling.

scholarly journals Modern Scientific Visualizations on the Web

Informatics ◽  
2020 ◽  
Vol 7 (4) ◽  
pp. 37
Author(s):  
Loraine Franke ◽  
Daniel Haehn
Keyword(s):  
Scientific Visualization ◽  
State Of The Art ◽  
Three Dimensional ◽  
Emerging Technology ◽  
Research Field ◽  
Future Directions ◽  
Web Based ◽  
Current State ◽  
Visualization Systems ◽  
The Web

Modern scientific visualization is web-based and uses emerging technology such as WebGL (Web Graphics Library) and WebGPU for three-dimensional computer graphics and WebXR for augmented and virtual reality devices. These technologies, paired with the accessibility of websites, potentially offer a user experience beyond traditional standalone visualization systems. We review the state-of-the-art of web-based scientific visualization and present an overview of existing methods categorized by application domain. As part of this analysis, we introduce the Scientific Visualization Future Readiness Score (SciVis FRS) to rank visualizations for a technology-driven disruptive tomorrow. We then summarize challenges, current state of the publication trend, future directions, and opportunities for this exciting research field.

Three-Dimensional Reconstruction of Two Forms of the Chaperonin GRO EL

1990 ◽  
Vol 48 (1) ◽  
pp. 258-259
Author(s):  
J.L. Carrascosa ◽  
G. Abella ◽  
S. Marco ◽  
M. Muyal ◽  
J.M. Carazo
Keyword(s):  
Three Dimensional ◽  
The Other ◽  
Two Dimensional ◽  
Series Method ◽  
Three Dimensional Reconstruction ◽  
Structural Components ◽  
E Coli ◽  
Dimensional Reconstruction ◽  
Morphogenetic Factors ◽  
Tilt Series

Chaperonins are a class of proteins characterized by their role as morphogenetic factors. They trantsiently interact with the structural components of certain biological aggregates (viruses, enzymes etc), promoting their correct folding, assembly and, eventually transport. The groEL factor from E. coli is a conspicuous member of the chaperonins, as it promotes the assembly and morphogenesis of bacterial oligomers and/viral structures.We have studied groEL-like factors from two different bacteria:E. coli and B.subtilis. These factors share common morphological features , showing two different views: one is 6-fold, while the other shows 7 morphological units. There is also a correlation between the presence of a dominant 6-fold view and the fact of both bacteria been grown at low temperature (32°C), while the 7-fold is the main view at higher temperatures (42°C). As the two-dimensional projections of groEL were difficult to interprete, we studied their three-dimensional reconstruction by the random conical tilt series method from negatively stained particles.

Identification, Prediction and Data Analysis of Noncoding RNAs: A Review

2019 ◽  
Vol 15 (3) ◽  
pp. 216-230 ◽  
Author(s):  
Abbasali Emamjomeh ◽  
Javad Zahiri ◽  
Mehrdad Asadian ◽  
Mehrdad Behmanesh ◽  
Barat A. Fakheri ◽  
...  
Keyword(s):  
Computational Methods ◽  
State Of The Art ◽  
Noncoding Rnas ◽  
Research Field ◽  
Design Strategies ◽  
Structural Prediction ◽  
Computational Costs ◽  
Cellular Processes ◽  
Laboratory Techniques ◽  
Fast Prediction

Background:Noncoding RNAs (ncRNAs) which play an important role in various cellular processes are important in medicine as well as in drug design strategies. Different studies have shown that ncRNAs are dis-regulated in cancer cells and play an important role in human tumorigenesis. Therefore, it is important to identify and predict such molecules by experimental and computational methods, respectively. However, to avoid expensive experimental methods, computational algorithms have been developed for accurately and fast prediction of ncRNAs.Objective:The aim of this review was to introduce the experimental and computational methods to identify and predict ncRNAs structure. Also, we explained the ncRNA’s roles in cellular processes and drugs design, briefly.Method:In this survey, we will introduce ncRNAs and their roles in biological and medicinal processes. Then, some important laboratory techniques will be studied to identify ncRNAs. Finally, the state-of-the-art models and algorithms will be introduced along with important tools and databases.Results:The results showed that the integration of experimental and computational approaches improves to identify ncRNAs. Moreover, the high accurate databases, algorithms and tools were compared to predict the ncRNAs.Conclusion:ncRNAs prediction is an exciting research field, but there are different difficulties. It requires accurate and reliable algorithms and tools. Also, it should be mentioned that computational costs of such algorithm including running time and usage memory are very important. Finally, some suggestions were presented to improve computational methods of ncRNAs gene and structural prediction.

scholarly journals Multi-hop assortativities for network classification

2018 ◽  
Vol 7 (4) ◽  
pp. 603-622 ◽  
Author(s):  
Leonardo Gutiérrez-Gómez ◽  
Jean-Charles Delvenne
Keyword(s):  
Machine Learning ◽  
Scientific Collaboration ◽  
State Of The Art ◽  
Medical Engineering ◽  
Research Field ◽  
Classification Task ◽  
Collaboration Network ◽  
Structural Patterns ◽  
Art Methods

Abstract Several social, medical, engineering and biological challenges rely on discovering the functionality of networks from their structure and node metadata, when it is available. For example, in chemoinformatics one might want to detect whether a molecule is toxic based on structure and atomic types, or discover the research field of a scientific collaboration network. Existing techniques rely on counting or measuring structural patterns that are known to show large variations from network to network, such as the number of triangles, or the assortativity of node metadata. We introduce the concept of multi-hop assortativity, that captures the similarity of the nodes situated at the extremities of a randomly selected path of a given length. We show that multi-hop assortativity unifies various existing concepts and offers a versatile family of ‘fingerprints’ to characterize networks. These fingerprints allow in turn to recover the functionalities of a network, with the help of the machine learning toolbox. Our method is evaluated empirically on established social and chemoinformatic network benchmarks. Results reveal that our assortativity based features are competitive providing highly accurate results often outperforming state of the art methods for the network classification task.

scholarly journals Topological correlators and surface defects from equivariant cohomology

2020 ◽  
Vol 2020 (9) ◽  
Author(s):  
Rodolfo Panerai ◽  
Antonio Pittelli ◽  
Konstantina Polydorou
Keyword(s):  
Quantum Mechanics ◽  
Equivariant Cohomology ◽  
Surface Defects ◽  
Star Product ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Dimensional System ◽  
The Novel ◽  
One Dimensional ◽  
Dual Quantum

Abstract We find a one-dimensional protected subsector of $$ \mathcal{N} $$ N = 4 matter theories on a general class of three-dimensional manifolds. By means of equivariant localization we identify a dual quantum mechanics computing BPS correlators of the original model in three dimensions. Specifically, applying the Atiyah-Bott-Berline-Vergne formula to the original action demonstrates that this localizes on a one-dimensional action with support on the fixed-point submanifold of suitable isometries. We first show that our approach reproduces previous results obtained on S3. Then, we apply it to the novel case of S2× S1 and show that the theory localizes on two noninteracting quantum mechanics with disjoint support. We prove that the BPS operators of such models are naturally associated with a noncom- mutative star product, while their correlation functions are essentially topological. Finally, we couple the three-dimensional theory to general $$ \mathcal{N} $$ N = (2, 2) surface defects and extend the localization computation to capture the full partition function and BPS correlators of the mixed-dimensional system.

scholarly journals Weak Interactions in Cocrystals of Isoniazid with Glycolic and Mandelic Acids

Crystals ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 328
Author(s):  
Raquel Álvarez-Vidaurre ◽  
Alfonso Castiñeiras ◽  
Antonio Frontera ◽  
Isabel García-Santos ◽  
Diego M. Gil ◽  
...  
Keyword(s):  
Density Functional ◽  
Glycolic Acid ◽  
Weak Interactions ◽  
Three Dimensional ◽  
Functional Theory ◽  
Molecular Systems ◽  
X Ray Crystallography ◽  
Hydroxycarboxylic Acids ◽  
Non Covalent Interactions ◽  
Covalent Interactions

This work deals with the preparation of pyridine-3-carbohydrazide (isoniazid, inh) cocrystals with two α-hydroxycarboxylic acids. The interaction of glycolic acid (H2ga) or d,l-mandelic acid (H2ma) resulted in the formation of cocrystals or salts of composition (inh)·(H2ga) (1) and [Hinh]+[Hma]–·(H2ma) (2) when reacted with isoniazid. An N′-(propan-2-ylidene)isonicotinic hydrazide hemihydrate, (pinh)·1/2(H2O) (3), was also prepared by condensation of isoniazid with acetone in the presence of glycolic acid. These prepared compounds were well characterized by elemental analysis, and spectroscopic methods, and their three-dimensional molecular structure was determined by single crystal X-ray crystallography. Hydrogen bonds involving the carboxylic acid occur consistently with the pyridine ring N atom of the isoniazid and its derivatives. The remaining hydrogen-bonding sites on the isoniazid backbone vary based on the steric influences of the derivative group. These are contrasted in each of the molecular systems. Finally, Hirshfeld surface analysis and Density-functional theory (DFT) calculations (including NCIplot and QTAIM analyses) have been performed to further characterize and rationalize the non-covalent interactions.

scholarly journals Extrusion Based 3D Printing of Sustainable Biocomposites from Biocarbon and Poly(trimethylene terephthalate)

Molecules ◽  
2021 ◽  
Vol 26 (14) ◽  
pp. 4164
Author(s):  
Elizabeth Diederichs ◽  
Maisyn Picard ◽  
Boon Peng Chang ◽  
Manjusri Misra ◽  
Amar Mohanty
Keyword(s):  
Mechanical Properties ◽  
3D Printing ◽  
Surface Finish ◽  
Three Dimensional ◽  
Morphological Properties ◽  
Great Promise ◽  
Structural Components ◽  
Computer Aided ◽  
Trimethylene Terephthalate ◽  
Optimal Quantity

Three-dimensional (3D) printing manufactures intricate computer aided designs without time and resource spent for mold creation. The rapid growth of this industry has led to its extensive use in the automotive, biomedical, and electrical industries. In this work, biobased poly(trimethylene terephthalate) (PTT) blends were combined with pyrolyzed biomass to create sustainable and novel printing materials. The Miscanthus biocarbon (BC), generated from pyrolysis at 650 °C, was combined with an optimized PTT blend at 5 and 10 wt % to generate filaments for extrusion 3D printing. Samples were printed and analyzed according to their thermal, mechanical, and morphological properties. Although there were no significant differences seen in the mechanical properties between the two BC composites, the optimal quantity of BC was 5 wt % based upon dimensional stability, ease of printing, and surface finish. These printable materials show great promise for implementation into customizable, non-structural components in the electrical and automotive industries.

scholarly journals Small footprint optoelectrodes using ring resonators for passive light localization

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Vittorino Lanzio ◽  
Gregory Telian ◽  
Alexander Koshelev ◽  
Paolo Micheletti ◽  
Gianni Presti ◽  
...  
Keyword(s):  
State Of The Art ◽  
Three Dimensional ◽  
Network Activity ◽  
Ring Resonators ◽  
Spatiotemporal Resolution ◽  
Optical Ring Resonators ◽  
Light Localization ◽  
Order Of Magnitude ◽  
Small Footprint

AbstractThe combination of electrophysiology and optogenetics enables the exploration of how the brain operates down to a single neuron and its network activity. Neural probes are in vivo invasive devices that integrate sensors and stimulation sites to record and manipulate neuronal activity with high spatiotemporal resolution. State-of-the-art probes are limited by tradeoffs involving their lateral dimension, number of sensors, and ability to access independent stimulation sites. Here, we realize a highly scalable probe that features three-dimensional integration of small-footprint arrays of sensors and nanophotonic circuits to scale the density of sensors per cross-section by one order of magnitude with respect to state-of-the-art devices. For the first time, we overcome the spatial limit of the nanophotonic circuit by coupling only one waveguide to numerous optical ring resonators as passive nanophotonic switches. With this strategy, we achieve accurate on-demand light localization while avoiding spatially demanding bundles of waveguides and demonstrate the feasibility with a proof-of-concept device and its scalability towards high-resolution and low-damage neural optoelectrodes.

Optimization of the Wrist Pin End of an Automobile Engine Connecting Rod With an Interference Fit

1990 ◽  
Vol 112 (3) ◽  
pp. 406-412 ◽  
Author(s):  
Vijay Sarihan ◽  
Ji Oh Song
Keyword(s):  
Finite Element ◽  
Optimum Design ◽  
Three Dimensional ◽  
Stress Singularity ◽  
Design Strategy ◽  
Structural Components ◽  
Connecting Rod ◽  
Fem Model ◽  
Automobile Engine ◽  
Interference Fit

Current design procedures for complicated three-dimensional structural components with component interactions may not necessarily result in optimum designs. The wrist pin end design of the connecting rod with an interference fit is governed by the stress singularity in the region where the wrist pin breaks contact with the connecting rod. Similar problems occur in a wide variety of structural components which involve interference fits. For a better understanding of the problems associated with obtaining optimum designs for this important class of structural interaction only the design problems associated with the wrist pin end of the rod are addressed in this study. This paper demonstrates a procedure for designing a functional and minimum weight wrist pin end of an automobile engine connecting rod with an interference fit wrist pin. Current procedures for Finite Element Method (FEM) model generation in complicated three-dimensional components are very time consuming especially in the presence of stress singularities. Furthermore the iterative nature of the design process makes the process of developing an optimum design very expensive. This design procedure uses a generic modeler to generate the FEM model based on the values of the design variables. It uses the NASTRAN finite element program for structural analysis. A stress concentration factor approach is used to obtain realistic stresses in the region of the stress singularity. For optimization, the approximate optimization strategy in the COPES/CONMIN program is used to generate an approximate design surface, determine the design sensitivities for constrained function minimization and obtain the optimum design. This proposed design strategy is fully automated and requires only an initial design to generate the optimum design. It does not require analysis code modifications to compute the design sensitivities and requires very few costly NASTRAN analyses. The connecting rod design problem was solved as an eight design variable problem with five constraints. A weight reduction of nearly 27 percent was achieved over an existing design and required only thirteen NASTRAN analyses. It is felt that this design strategy can be effectively used in an engineering environment to generate optimum designs of complicated three-dimensional components.

Sign in / Sign up

Export Citation Format

Share Document