Basic Overview of Chemoinformatics

Engel, Thomas

doi:10.1021/ci600234z

Cited by 130 publications

(70 citation statements)

References 164 publications

(230 reference statements)

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“…The 1998 starting point is thus rather arbitrary in nature and the interested reader is referred to several accounts (Chen 2006;Engel 2006;Willett 2003) that describe the historical development of the subject and of its core technologies, e.g., the use of graph, statistical and expert-system methods for searching chemical structure databases, for predicting biological activity, and designing synthetic pathways, respectively.…”

Section: Introductionmentioning

confidence: 99%

“…These programmes involve the synthesis of large numbers of In this paper, we shall take 1998 as the starting point for our analysis, as this was when Brown's first formal definition of chemoinformatics appeared. That said, many of the basic techniques in chemoinformatics were developed prior to that date; indeed, the title of the paper by Hann and Green (1999) is "Chemoinformatics -a new name for an old problem".The 1998 starting point is thus rather arbitrary in nature and the interested reader is referred to several accounts (Chen 2006;Engel 2006;Willett 2003) that describe the historical development of the subject and of its core technologies, e.g., the use of graph, statistical and expert-system methods for searching chemical structure databases, for predicting biological activity, and designing synthetic pathways, respectively. …”

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confidence: 99%

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A bibliometric analysis of the literature of chemoinformatics

Willett

2008

Aslib Proceedings

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Abstract.Purpose: To analyse the literature of chemoinformatics, a subject that has arisen over the last few years and that draws on techniques from a range of disciplines, most notably chemistry (particularly computational and medicinal chemistry), computer science and information science. Method: Subject, author and citation searches of (principally) the Web of Knowledge database. Findings:The Journal of Chemical Information and Modeling (previously the Journal of Chemical Information and Computer Sciences) is the core journal for the subject, but with many significant papers being published in journals whose principal focus is molecular modelling, quantitative structure-activity relationships or more general aspects of chemistry. The discipline is international in scope, and many of the most cited papers describe software packages that play a key role in modern chemoinformatics research Originality: This is the first bibliometric study of chemoinformatics, and one of only a very few that consider the bibliometrics of computational chemistry more generally. Paper Type Research paper KeywordsAuthor productivity, Bibliometrics, cheminformatics, chemoinformatics, citation analysis INTRODUCTION Chemical information has been processed and exploited for many years, first in printed (Cooke, 2004) and then in computer form Hann and Green 1999). It is now, under the name of chemoinformatics, a key component of modern chemical research (Gasteiger and Engels, 2003;Leach and Gillet, 2003). Chemoinformatics' enhanced role has come about principally from the vast increase that has occurred in the volumes of data that need to be stored, searched and mined in research programmes for the discovery of biologically active molecules, most obviously but not exclusively in the pharmaceutical and agrochemical industries. These programmes involve the synthesis of large numbers of In this paper, we shall take 1998 as the starting point for our analysis, as this was when Brown's first formal definition of chemoinformatics appeared. That said, many of the basic techniques in chemoinformatics were developed prior to that date; indeed, the title of the paper by Hann and Green (1999) is "Chemoinformatics -a new name for an old problem".The 1998 starting point is thus rather arbitrary in nature and the interested reader is referred to several accounts (Chen 2006;Engel 2006;Willett 2003) that describe the historical development of the subject and of its core technologies, e.g., the use of graph, statistical and expert-system methods for searching chemical structure databases, for predicting biological activity, and designing synthetic pathways, respectively.

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Section: Introductionmentioning

confidence: 99%

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confidence: 99%

A bibliometric analysis of the literature of chemoinformatics

Willett

2008

Aslib Proceedings

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“…[14], [18], [10]. Other types of representations include MOL and SDF formats for single and multiple molecules, respectively.…”

Section: Molecular Structure Representationsmentioning

confidence: 99%

A Fully Reversible Data Transform Technique Enhancing Data Compression of SMILES Data

Scanlon

Ridley

2013

Availability, Reliability, and Security in Information Systems and HCI

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Abstract. The requirement to efficiently store and process SMILES data used in Chemoinformatics creates a demand for efficient techniques to compress this data. General-purpose transforms and compressors are available to transform and compress this type of data to a certain extent, however, these techniques are not specific to SMILES data. We develop a transform specific to SMILES data that can be used alongside other general-purpose compressors as a preprocessor and post-processor to improve the compression of SMILES data. We test our transform with six other general-purpose compressors and also compare our results with another transform on our SMILES data corpus, we also compare our results with untransformed data.Keywords: SMILES, Data Transform, Data Compression. IntroductionThe Simplified Molecular Input Line Entry System (SMILES) language was developed to represent two-dimensional molecular structures in a concise and compact way allowing for storage and processing improvements. General-purpose compressors allow for further reductions in storage and processing costs [23], [8].With the continuous expansion of chemical databases [15] and the need for efficient storage and searching of molecular structure representations, such as SMILES [23], [8], storage and processing costs of these representations need to be further improved.Data can be transformed by exploiting the specific information contained in the data to its advantage. Transformed data can be used alongside general-purpose compression techniques to further improve compression results [21], [4], [20].We make the following contributions in this paper:• We present our SMILES-specific transform designed to enhance the compression of SMILES data when used with other general-purpose compressors.• We provide results from using general-purpose compression techniques on a breakdown of different SMILES transform scenarios and a combination of techniques used in our SMILES transforms.

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“…In other words this is a sub-graph isomorphism problem [112], quite similar to the search of chemical substructures, discussed since the 1960s by chemistry informatics (see Engel [113] for a review). Although there exist several sophisticated algorithms to perform this kind of computation [114], we use a much simpler algorithm here, due to the fact that chemical diversity is not accounted for in the united atoms model and thus the task can be performed with less effort.…”

Section: Determination Of the Architecture Coefficientsmentioning

confidence: 99%