Web Apps Come of Age for Molecular Sciences

Abriata, Luciano A.

doi:10.3390/informatics4030028

Cited by 24 publications

(24 citation statements)

References 67 publications

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“…In the online visualization, different models can be compared by clicking on the score correlation plots or on the list of proposed top clusters. Being based on standard web app technologies in a single HTML document, this web app could be the starting point for future tools that facilitate model navigation and evaluation online at the Prediction Center, adding to the array of available tools.…”

Section: Methodsmentioning

confidence: 99%

Assessment of hard target modeling in CASP12 reveals an emerging role of alignment‐based contact prediction methods

et al. 2017

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We present our assessment of CASP12 modeling efforts for targets with no obvious templates of high sequence/structure similarity in the PDB, that is for evaluation units of the free modeling (FM) and free modeling/template‐based modeling (FM/TBM) categories. Models were clustered and ranked using the Global Distance Test‐Total Score and 5 additional metrics developed in previous CASP rounds, producing short lists of models that were subject to visual inspection in comparison to the target structures. The whole procedure was implemented as a web app that facilitates model selection and visual inspection, and could become useful to facilitate and standardize future assessments. We describe cases of (1) targets with remarkably good predictions, (2) targets whose models captured some global shape and topology features, and (3) targets for which models fail to capture even coarse features. We note that despite this CASP being among the most challenging ones, a measurable improvement of the top predictions is apparent, that we attribute to the emergence of accurate contact prediction methods and the increased number of available sequences. We also briefly discuss current limitations in tertiary structure prediction exemplified by CASP12 targets. Overall, the Baker, Zhang, and Lee manual groups and servers were identified as the top global performing groups.

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Section: Methodsmentioning

confidence: 99%

Assessment of hard target modeling in CASP12 reveals an emerging role of alignment‐based contact prediction methods

et al. 2017

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“…The Microsoft team plans to add more languages over time. This JavaScript API can also provide several basic ways for accessing data in a client-side MS-Office file to get and set the selected data, or to get access to the entire range of documents [15].…”

Section: Methodsmentioning

confidence: 99%

Apps-based Machine Translation on Smart Media Devices - A Review

Gunarto

2019

Indonesian J. Comput. Cybern. Syst.

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Machine Translation Systems are part of Natural Language Processing (NLP) that makes communication possible among people using their own native language through computer and smart media devices. This paper describes recent progress in language dictionaries and machine translation commonly used for communications and social interaction among people or Internet users worldwide who speak different languages. Problems of accuracy and quality related to computer translation systems encountered in web & Apps-based translation are described and discussed. Possible programming solutions to the problems are also put forward to create software tools that are able to analyze and synthesize language intelligently based on semantic representation of sentences and phrases. Challenges and problems on Apps-based machine translation on smart devices towards AI, NLP, smart learning and understanding still remain until now, and need to be addressed and solved through collaboration between computational linguists and computer scientists.

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“…As recently reviewed in a dedicated issue of Computing and Science in Engineering (M. DiPierro, 2018), JavaScript has become very powerful by including language subsets specialized for speed, optimized just-in-time compilation, methods to program background scripts, and libraries to perform multi-core and on-GPUs computing to accelerate intensive calculations. It is in fact now possible to transpile from C/C++ and other languages directly to JavaScript retaining close-tonative execution speeds, allowing web browsers to support quite complex data analysis and visualization directly in web pages (Abriata et al, 2017;Abriata, 2017a). This opens up the possibility of simulating molecular mechanics and experimental data, performing numerical data analysis and even handling data in neural networks, directly inside the molecular modeling web app to enable real-time feedback as the user manipulates the molecular systems.…”

Section: Intensive Calculationsmentioning

confidence: 99%

“…Rather than manually implementing calculations, a number of libraries are now available for specific applications that help to save code writing time and bring the additional advantage of being developed by specialists (Abriata, 2017a). One particularly useful library in the scope of this paper is Cannon.js (https://schteppe.github.io/cannon.js/), an engine for simulating rigid body mechanics that integrates with Three.js and A-Frame.…”

Section: Intensive Calculationsmentioning

confidence: 99%

Peer Review #2 of "Building blocks for commodity augmented reality-based molecular visualization and modeling in web browsers (v0.1)"

Sommer¹

2020

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For years, immersive interfaces using virtual and augmented reality (AR) for molecular visualization and modeling have promised a revolution in the way how we teach, learn, communicate and work in chemistry, structural biology and related areas. However, most tools available today for immersive modeling require specialized hardware and software, and are costly and cumbersome to setup. These limitations prevent wide use of immersive technologies in education and research centers in a standardized form, which in turn prevents large-scale testing of the actual effects of such technologies on learning and thinking processes. Here, I discuss building blocks for creating marker-based AR applications that run as web pages on regular computers, and explore how they can be exploited to develop web content for handling virtual molecular systems in commodity AR with no more than a webcam-and internet-enabled computer. Examples span from displaying molecules, electron microscopy maps and molecular orbitals with minimal amounts of HTML code, to incorporation of molecular mechanics, real-time estimation of experimental observables and other interactive resources using JavaScript. These web apps provide virtual alternatives to physical, plastic-made molecular modeling kits, where the computer augments the experience with information about spatial interactions, reactivity, energetics, etc. The ideas and prototypes introduced here should serve as starting points for building active content that everybody can utilize online at minimal cost, providing novel interactive pedagogic material in such an open way that it could enable mass-testing of the effect of immersive technologies on chemistry education.

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Web Apps Come of Age for Molecular Sciences

Cited by 24 publications

References 67 publications

Assessment of hard target modeling in CASP12 reveals an emerging role of alignment‐based contact prediction methods

Assessment of hard target modeling in CASP12 reveals an emerging role of alignment‐based contact prediction methods

Apps-based Machine Translation on Smart Media Devices - A Review

Peer Review #2 of "Building blocks for commodity augmented reality-based molecular visualization and modeling in web browsers (v0.1)"

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