scholarly journals 3dRS, a Web-Based Tool to Share Interactive Representations of 3D Biomolecular Structures and Molecular Dynamics Trajectories

2021 ◽  
Vol 8 ◽  
Author(s):  
Genís Bayarri ◽  
Adam Hospital ◽  
Modesto Orozco
Keyword(s):  
Molecular Dynamics ◽  
Structural Data ◽  
Control Panel ◽  
Data Streaming ◽  
Web Based ◽  
Scientific Papers ◽  
Multiple Structures ◽  
3D Representation ◽  
Server Design ◽  
Definition Of

3D Representation Sharing (3dRS) is a web-based tool designed to share biomolecular structure representations, including 4D ensembles derived from Molecular Dynamics (MD) trajectories. The server offers a team working in different locations a single URL to share and discuss structural data in an interactive fashion, with the possibility to use it as a live figure for scientific papers. The web tool allows an easy upload of structures and trajectories in different formats. The 3D representation, powered by NGL viewer, offers an interactive display with smooth visualization in modern web browsers. Multiple structures can be loaded and superposed in the same scene. 1D sequences from the loaded structures are presented and linked to the 3D representation. Multiple, pre-defined 3D molecular representations are available. The powerful NGL selection syntax allows the definition of molecular regions that can be then displayed using different representations. Important descriptors such as distances or interactions can be easily added into the representation. Trajectory frames can be explored using a common video player control panel. Trajectories are efficiently stored and transferred to the NGL viewer thanks to an MDsrv-based data streaming. The server design offers all functionalities in one single web page, with a curated user experience, involving a minimum learning curve. Extended documentation is available, including a gallery with a collection of scenes. The server requires no registration and is available at https://mmb.irbbarcelona.org/3dRS.

scholarly journals The Structural Versatility of the BTB Domains of KCTD Proteins and Their Recognition of the GABAB Receptor

Biomolecules ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 323 ◽  
Author(s):  
Nicole Balasco ◽  
Giovanni Smaldone ◽  
Luigi Vitagliano
Keyword(s):  
Molecular Dynamics ◽  
Gabab Receptor ◽  
Structural Data ◽  
Md Simulations ◽  
Functional Roles ◽  
Dynamic View ◽  
Definition Of ◽  
Dynamics Simulations ◽  
Structural Versatility ◽  
Btb Domains

Several recent investigations have demonstrated that members of the KCTD (Potassium Channel Tetramerization Domain) protein family are involved in fundamental processes. However, the paucity of structural data available on these proteins has frequently prevented the definition of their biochemical role(s). Fortunately, this scenario is rapidly changing as, in very recent years, several crystallographic structures have been reported. Although these investigations have provided very important insights into the function of KCTDs, they have also raised some puzzling issues. One is related to the observation that the BTB (broad-complex, tramtrack, and bric-à-brac) domain of these proteins presents a remarkable structural versatility, being able to adopt a variety of oligomeric states. To gain insights into this intriguing aspect, we performed extensive molecular dynamics simulations on several BTB domains of KCTD proteins in different oligomeric states (monomers, dimers, tetramers, and open/close pentamers). These studies indicate that KCTD-BTB domains are stable in the simulation timescales, even in their monomeric forms. Moreover, simulations also show that the dynamic behavior of open pentameric states is strictly related to their functional roles and that different KCTDs may form stable hetero-oligomers. Molecular dynamics (MD) simulations also provided a dynamic view of the complex formed by KCTD16 and the GABAB2 receptor, whose structure has been recently reported. Finally, simulations carried out on the isolated fragment of the GABAB2 receptor that binds KCTD16 indicate that it is able to assume the local conformation required for the binding to KCTD.

scholarly journals Studies of Conformational Changes of Tubulin Induced by Interaction with Kinesin Using Atomistic Molecular Dynamics Simulations

2021 ◽  
Vol 22 (13) ◽  
pp. 6709
Author(s):  
Xiao-Xuan Shi ◽  
Peng-Ye Wang ◽  
Hong Chen ◽  
Ping Xie
Keyword(s):  
Molecular Dynamics ◽  
High Resolution ◽  
Binding Energy ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
Weak Interactions ◽  
Molecular Motor ◽  
Structural Data ◽  
Calculated Binding Energy ◽  
Dynamics Simulations

The transition between strong and weak interactions of the kinesin head with the microtubule, which is regulated by the change of the nucleotide state of the head, is indispensable for the processive motion of the kinesin molecular motor on the microtubule. Here, using all-atom molecular dynamics simulations, the interactions between the kinesin head and tubulin are studied on the basis of the available high-resolution structural data. We found that the strong interaction can induce rapid large conformational changes of the tubulin, whereas the weak interaction cannot. Furthermore, we found that the large conformational changes of the tubulin have a significant effect on the interaction of the tubulin with the head in the weak-microtubule-binding ADP state. The calculated binding energy of the ADP-bound head to the tubulin with the large conformational changes is only about half that of the tubulin without the conformational changes.

scholarly journals The identity of a new profession

2020 ◽  
Vol 4 (1) ◽  
Author(s):  
Brenda Le ◽  
Darren Tellier
Keyword(s):  
Chinese Medicine ◽  
Health Professions ◽  
Mixed Methods Study ◽  
Professional Organizations ◽  
Structured Interviews ◽  
Web Based ◽  
Education Practice ◽  
Healthcare Needs ◽  
Definition Of ◽  
Medical Traditions

In Canada, there is a growing interest in regulating the practices of acupuncture and Chinese herbology under the banner of ‘Traditional Chinese Medicine’ (TCM). However, the origins and definition of TCM are unclear and therefore disputed. While TCM is often used as an umbrella term to represent Chinese medical traditions that span millennia, numerous academics consider TCM to be a modern construct that has departed from the foundational roots of Chinese medicine. To better understand TCM and its implications for the profession, our study investigates: 1) historical precedents leading up to the formal creation of TCM; 2) characteristics and defining features of TCM; and 3) how this relates to education, practice and regulation of the profession in Canada. A mixed-methods study design was employed. Semi-structured interviews were conducted to explore perceptions of individuals who contributed to mediums that discussed the formation of TCM or traditions that exist outside of TCM. In addition, an anonymous web-based survey was sent to TCM-related professional organizations, who were asked to distribute the survey to their members to capture the views of persons practicing within TCM-related health professions in Canada. Due to a lack of participation from the organizations, no survey data was collected. Interviews revealed that TCM is a product of the standardization and simplification of Chinese medicine during the 1950’s and 60’s in China to meet healthcare needs at the time. Currently in Canada, there appears to be a lack of awareness that the establishment of TCM is not a comprehensive representation of Chinese medical traditions, and that many aspects of it may not be suited to the healthcare landscape of modern-day Canada. There is a need for more discussion surrounding the identity of this new profession.

scholarly journals WONKAandOOMMPPAA: analysis of protein–ligand interaction data to direct structure-based drug design

2017 ◽  
Vol 73 (3) ◽  
pp. 279-285
Author(s):  
Charlotte M. Deane ◽  
Ian D. Wall ◽  
Darren V. S. Green ◽  
Brian D. Marsden ◽  
Anthony R. Bradley
Keyword(s):  
Three Dimensional ◽  
Structural Data ◽  
Data Sets ◽  
Interaction Data ◽  
Activity Data ◽  
Ligand Interaction ◽  
Structure Based Drug Design ◽  
Web Based ◽  
Protein Ligand Interaction ◽  
Ligand Activity

In this work, two freely available web-based interactive computational tools that facilitate the analysis and interpretation of protein–ligand interaction data are described. Firstly,WONKA, which assists in uncovering interesting and unusual features (for example residue motions) within ensembles of protein–ligand structures and enables the facile sharing of observations between scientists. Secondly,OOMMPPAA, which incorporates protein–ligand activity data with protein–ligand structural data using three-dimensional matched molecular pairs.OOMMPPAAhighlights nuanced structure–activity relationships (SAR) and summarizes available protein–ligand activity data in the protein context. In this paper, the background that led to the development of both tools is described. Their implementation is outlined and their utility using in-house Structural Genomics Consortium (SGC) data sets and openly available data from the PDB and ChEMBL is described. Both tools are freely available to use and download at http://wonka.sgc.ox.ac.uk/WONKA/ and http://oommppaa.sgc.ox.ac.uk/OOMMPPAA/.

scholarly journals Structure and Dynamics of Zr4+ in Aqueous Solution: An Ab Initio QM/MM Molecular Dynamics Study

2015 ◽  
Vol 15 (2) ◽  
pp. 155-162 ◽  
Author(s):  
Suwardi Suwardi ◽  
Harno Dwi Pranowo ◽  
Ria Armunanto
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Distribution Function ◽  
Pair Potential ◽  
Structural Data ◽  
Angular Distribution Function ◽  
Dilute Aqueous Solution ◽  
Dynamical Properties ◽  
Experimental Values ◽  
Three Body

A QM/MM molecular dynamics (MD) simulation has been carried out using three-body corrected pair potential to investigate the structural and dynamical properties of Zr4+ in dilute aqueous solution. Structural data in the form of radial distribution function, coordination number distribution, and angular distribution function were obtained. The results indicate eight water molecules coordinate to zirconium ion and have two angles of O-Zr4+-O, i.e. 72.0° and 140.0° with a Zr4+-O distance of 2.34 Å. According to these results, the hydration structure of Zr4+ ion in water was more or less well-defined square antiprismatic geometry. The dynamical properties have been characterized by the ligand’s mean residence time (MRT) and Zr4+-O stretching frequencies. The inclusion of the three-body correction was important for the description of the hydrated Zr4+ ion, and the results indicated in good agreement with experimental values.

scholarly journals Design-Based Research: Definition, Characteristics, Application and Challenges

2019 ◽  
Vol 5 (1) ◽  
pp. 26-35
Author(s):  
Hamed Vaezi ◽  
Hossein Karimi Moonaghi ◽  
Reyhaneh Golbaf
Keyword(s):  
Medical Education ◽  
Practical Knowledge ◽  
Educational Innovation ◽  
Sources Of Information ◽  
Multiple Sources ◽  
Short Term ◽  
Web Based ◽  
Design Based Research ◽  
Definition Of ◽  
New Research

In recent years medical education has developed dramatically, but lecturers often cite the existence of a gap between theoretical and practical knowledge. In the first decade of the present century, new research methodology named “design-based research (DBR)” was developed, which most experts and journals refer to as a fundamental way to make changes in the quality and applicability of studies and educational research as well as to enhance and improve the practice of instruction. The aim of the present study was introducing design-based research and its concepts, features, applications, and challenges. A narrative review was conducted in 2018. For this purpose, authorized English academic database including Web of Science, Science Direct, Google Scholar, international database and library in medical research filed with keywords including “design-based research, definition of DBR, DBR applications, medical education, and DBR challenges” without date limitation until 2018.11.21 were screened. Overall, 68 articles were selected and after careful reading, 21 article with related subjects were selected for material extraction. The conclusion was made that DBR that combines empirical research with design-based theories could be considered as an effective method for understanding quality, time and the cause of the phenomenon of educational innovation in practice. Usually DBR is formed by initial evaluation of a problem that occurs in a particular context, and this assessment continues throughout design and implementation. One of the characteristics of DBR is the guiding team, which includes researchers, professionals, designers, managers, teachers, trainers and others whose expertise and knowledge may in some way help. The application of DBR in web-based training programs is quite evident. The probability of non-returns in short-term projects is one of the main challenges of DBR. Medical education has developed dramatically in recent years, but it has made little progress in promoting innovative research methodologies. DBR can be used as a bridge between theories and practice and provide the basis for close communication between researchers, designers, and participants. By applying sophisticated methods and multiple sources of information, the success rate of an intervention in a particular environment is assessed, which ultimately leads to improved theories.

scholarly journals Occupational exoskeletons: A roadmap toward large-scale adoption. Methodology and challenges of bringing exoskeletons to workplaces

2021 ◽  
Vol 2 ◽  
Author(s):  
Simona Crea ◽  
Philipp Beckerle ◽  
Michiel De Looze ◽  
Kevin De Pauw ◽  
Lorenzo Grazi ◽  
...  
Keyword(s):  
Large Scale ◽  
Health And Safety ◽  
Field Studies ◽  
Specific Work ◽  
Safety Standards ◽  
Knowledge Based ◽  
Scientific Papers ◽  
Large Scale Field ◽  
Standards And Regulations ◽  
Definition Of

Abstract The large-scale adoption of occupational exoskeletons (OEs) will only happen if clear evidence of effectiveness of the devices is available. Performing product-specific field validation studies would allow the stakeholders and decision-makers (e.g., employers, ergonomists, health, and safety departments) to assess OEs’ effectiveness in their specific work contexts and with experienced workers, who could further provide useful insights on practical issues related to exoskeleton daily use. This paper reviews present-day scientific methods for assessing the effectiveness of OEs in laboratory and field studies, and presents the vision of the authors on a roadmap that could lead to large-scale adoption of this technology. The analysis of the state-of-the-art shows methodological differences between laboratory and field studies. While the former are more extensively reported in scientific papers, they exhibit limited generalizability of the findings to real-world scenarios. On the contrary, field studies are limited in sample sizes and frequently focused only on subjective metrics. We propose a roadmap to promote large-scale knowledge-based adoption of OEs. It details that the analysis of the costs and benefits of this technology should be communicated to all stakeholders to facilitate informed decision making, so that each stakeholder can develop their specific role regarding this innovation. Large-scale field studies can help identify and monitor the possible side-effects related to exoskeleton use in real work situations, as well as provide a comprehensive scientific knowledge base to support the revision of ergonomics risk-assessment methods, safety standards and regulations, and the definition of guidelines and practices for the selection and use of OEs.

B2B, B2C and Virtual Enterprise Management Systems

2020 ◽  
pp. 118-127
Author(s):  
Yong Geng Chen
Keyword(s):  
Virtual Enterprise ◽  
Enterprise Management ◽  
Virtual Enterprises ◽  
Future Directions ◽  
Web Based ◽  
Goods And Services ◽  
Detailed Evaluation ◽  
Business To Consumer ◽  
Definition Of ◽  
Business To Business

This research paper provides a detailed evaluation of the business concepts in Electronic Commerce (E-Commerce). The concept of E-Commerce defines the exchange of goods and services with monetary value between consumers and companies. E-Commerce is a web-based catalogue whereby buyers can possibly place order and sellers possibly accept payments. E-Commerce incorporates two forms of business: Business-to-Business (B2B) and Business-to-Consumer (B2C), which provides a definition of the commerce transactions between enterprises, such as between the wholesalers and the manufacturers or the retailers. B2C E-Commerce provides enterprises with the model which allows businesses to deliver purchasers to the relevant merchants and achieve from the commission rewards given by the merchants. This paper evaluates two forms of business with relation to management of Virtual Enterprises (VE) in the field of E-Commerce. The paper will end with an analysis of VE before projecting future directions for health of B2B and B2C in business.

Using New Technologies to Engage and Support English Language Learners in Mathematics Classrooms

2019 ◽  
pp. 549-563
Author(s):  
Robert Pritchard ◽  
Susan O'Hara ◽  
Jeff Zwiers
Keyword(s):  
English Language Learners ◽  
Language Learners ◽  
English Language ◽  
New Technologies ◽  
Academic Language ◽  
Mathematical Practice ◽  
Web Based ◽  
Mathematics Classrooms ◽  
Grade Levels ◽  
Definition Of

An emerging body of research is demonstrating the potential of new technologies such as iPad and phone apps, wikis, blogs, podcasts and web-based editing tools for significantly improving the academic language development of English language learners. The authors of this chapter present an expanded definition of academic language, explain why these new technologies are important, and discuss how they can be used to provide effective and innovative mathematics instruction to English language learners. Three classroom vignettes demonstrate specific ways in which a variety of technologies can be implemented across grade levels to meet the Common Core State Standards for Mathematical Practice and Content.

Interactive Web-Based Tools for Learning Mathematics

2012 ◽  
pp. 274-306
Author(s):  
Barry Cherkas ◽  
Rachael M. Welder
Keyword(s):  
Mathematics Teachers ◽  
Dynamic Capabilities ◽  
Preservice Teacher Education ◽  
Mathematical Concepts ◽  
Web Based ◽  
Working Definition ◽  
Learning Mathematics ◽  
Collegiate Mathematics ◽  
Definition Of ◽  
Interactive Resources

There is an abundance of Web-based resources designed for mathematics teachers and learners at every level. Some of these are static, while others are interactive or dynamic, giving mathematics learners opportunities to develop visualization skills, explore mathematical concepts, and obtain solutions to self-selected problems. Research into the efficacy of online mathematics demonstrations and interactive resources is lacking, but it is clear that not all online resources are equal from a pedagogical viewpoint. In this chapter, a number of popular and relevant websites for collegiate mathematics and collegiate preservice teacher education are examined. They are reviewed and investigated in terms of their interactivity, dynamic capabilities, pedagogical strengths and weaknesses, the practices they employ, and their potential to enhance mathematical learning both inside and outside of the collegiate classroom. Culled from these reviews is a working definition of “best practices”: condensing difficult mathematical concepts into representations and models that clarify ideas with minimal words, thereby enabling a typical student to grasp, quickly and easily, the underlying mathematics.

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