Programming languages in chemistry: a review of HTML5/JavaScript

Theisen, Kevin J.

doi:10.1186/s13321-019-0331-1

Cited by 15 publications

(13 citation statements)

References 13 publications

(12 reference statements)

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“…The ligand moiety, N3 was docked non-covalently in the co-crystallized form of its original position in 6LU7.PB with the resulting RMSD 1.66 Å as determined from the DockRMSD tool ( Fig. 1 -b) [26] . The docking software used was AutoDock 4.2 [27] .…”

Section: Methodsmentioning

confidence: 99%

Evaluation of SARS-CoV-2 main protease and inhibitor interactions using dihedral angle distributions and radial distribution function

Lamichhane

Ghimire

2021

Heliyon

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Section: Methodsmentioning

confidence: 99%

Evaluation of SARS-CoV-2 main protease and inhibitor interactions using dihedral angle distributions and radial distribution function

Lamichhane

Ghimire

2021

Heliyon

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“…Because it uses JSON [18] as the encoding method, implementing basic read/write/modify operations is simple and convenient in most modern programming languages. JSON is a very popular serialisation technique, and it is not only ubiquitous and easy to manipulate programmatically, but is also relatively concise and human readable [19, 20]. More detailed editing and analysis introduces the dependency on the Molfile (aka CTAB) structure representation, and compliance with the specification rules for specifying quantities.…”

Section: Methodsmentioning

confidence: 99%

“…The quantity field can be given as a single number or as a range (an array of two numbers, e.g. [10, 20] to denote between 10 and 20). The relation field can be defined when the quantity number is other than a point value, e.g.…”

Section: Methodsmentioning

confidence: 99%

Capturing mixture composition: an open machine-readable format for representing mixed substances

et al. 2019

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We describe a file format that is designed to represent mixtures of compounds in a way that is fully machine readable. This Mixfile format is intended to fill the same role for substances that are composed of multiple components as the venerable Molfile does for specifying individual structures. This much needed datastructure is intended to replace current practices for communicating information about mixtures, which usually relies on human-readable text descriptions, drawing several species within a single molecular diagram, or mutually incompatible ad hoc solutions. We describe an open source software application for editing mixture files, which can also be used as web-ready tools for manipulating the file format. We also present a corpus of mixture examples, which we have extracted from collections of text-based descriptions. Furthermore, we present an early look at the proposed IUPAC Mixtures InChI specification, instances of which can be automatically generated using the Mixfile format as a precursor.

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“…Для реализации веб-приложения, с которым будет работать клиент, был выбран язык программирования JavaScript [13], так как альтернативы для данной задачи не существует, а реа- лизация WebAssembly, с помощью которого можно писать клиентские веб-приложения на C++, пока что находится в бета-режиме. Данный язык программирования обладает огромными преимуществами в области динамической работы с DOM (Document Object Model -объектная модель представления XML\HTML-документов) и работы по сети.…”

Section: обзор технологий для реализации клиентской частиunclassified

Developing of WebMCOT Web-Service for Finding Cooperative Site-Binding TF DNA-Motifs

Mukhin

Levitsky

Lashin

2019

JIT

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Regulation of eukaryotic gene transcription is controlled by specific proteins transcription factors. Transcription factors bind certain regions of genomic DNA (binding sites or motives). Common action of two or more transcription factors is widespread mechanism of transcription factor action. Hence, the term ‘composite element’ implied two closely located and frequently occurred in genomic DNA motives. Composite elements are partitioned onto those with two overlapped motifs, or with these two motifs separated with a spacer. Currently, the chromatin immunoprecipitation high throughput approach ChIP-seq is used to locate binding sites for a certain “anchor” transcription factor in vivo in genomic scale. Thus, the search of composite elements with the help of ChIP-seq whole-genome transcription factor binding profiles is the actual bioinformatics issue. But existing approaches for prediction of composite elements on the basis of ChIP-seq data either omit an overlap of motifs (but require only a single ChIP-seq dataset) or consider an overlap of motifs (but require additional ChIP-seq data for a partner motif). But, ChIP-seq experiments are very expensive. In the Institute of Cytology and Genetics, MCOT program has been recently developed. It performs search of motifs taking into account their overlaps based on a single ChIP-seq dataset. MCOT is a console application and does not have many user friendly functions like data preparation and report generation. This work presents a web service WebMCOT for prediction of co-occurred DNA motifs in ChIP-seq data. WebMCOT consists of three parts: client, server, and worker. Software tools list, architecture and web interface are presented.

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Programming languages in chemistry: a review of HTML5/JavaScript

Cited by 15 publications

References 13 publications

Evaluation of SARS-CoV-2 main protease and inhibitor interactions using dihedral angle distributions and radial distribution function

Evaluation of SARS-CoV-2 main protease and inhibitor interactions using dihedral angle distributions and radial distribution function

Capturing mixture composition: an open machine-readable format for representing mixed substances

Developing of WebMCOT Web-Service for Finding Cooperative Site-Binding TF DNA-Motifs

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