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This article is part of a Supplement: Volume 5 Supplement 1
This article is part of a Supplement: Volume 2 Supplement 1
This article is part of a Supplement: Volume 5 Supplement 1
PubChem is an open archive consisting of a ... . Currently (as of Nov. 2015), PubChem contains more than 150 million depositor-provided...
PubChem is an important public, Web-based information ... JavaScript functions, and image sequence streaming. The PubChem structure editor does not require the presence...
PubChem is an open repository for chemical structures, ... to distribute and integrate scientific data. Exposing PubChem data to Semantic Web services may help...
PubChem is a chemical information repository, consisting of ... structure standardization. The present study describes the PubChem standardization approaches and analyzes them for their ... structures during the ...
PubChem is a public repository for biological activities ... of its vast amount of chemical information, PubChem performs 2-dimensional (2-D) and ... precompute “neighbor” relationships between molecules in the PubChem
For our analysis, after hydrogen suppression, atoms were characterized by atomic number, formal charge, implicit hydrogen count, explicit degree (number of neighbors), valence (bond order sum), and aromaticity. B...
PubChem is a chemical data repository that provides ... with new opportunities for data-intensive research. PubChem provides several programmatic access routes. One of ... interface specialized for accessing anno...
...As one of the largest publicly accessible databases for hosting chemical structures and biological activities, PubChem has been processing bioassay submissions from the ... increase in volume for the deposited...
In this paper, we propose a scaffold hierarchy as a result of large-scale analysis of the PubChem Compound database. The analysis not only provided insights into scaffold diversity of the PubChem Compound databas...
Research discussed in the present paper employed a bioactivity-centered clustering approach to group 843,845 non-inactive compounds stored in PubChem according to both structural similarity and bioactivity ... wi...
PubChem is an open repository for small molecules and their experimental biological activity. PubChem integrates and provides search, retrieval, visualization, ... with similar biological efficacies against targe...
Where they could be calculated, extracted compounds-per-journal article were in the range of 12 to 19 but compound-per-protein counts increased with document numbers. Chemical structure filtration to facilitate s...
The Resource Description Framework (RDF), together with well-defined ontologies, significantly increases data interoperability and usability. The SPARQL query language was introduced to retrieve requested RDF dat...
The use of 3-D similarity techniques in the analysis of biological data and virtual screening is pervasive, but what is a biologically meaningful 3-D similarity value? Can one find statistically significant separ...
PubChem is a free and open public resource ... both chemical structures and biological test results, PubChem is a sizeable system with an uneven ... of available information. Some chemical structures in PubChem i...
Compound (or chemical) databases are an invaluable resource for many scientific disciplines. Exposomics researchers need to find and identify relevant chemicals that cover the entirety of potential (chemical and ...
To improve the utility of PubChem, a public repository containing biological activities of ... to the small-molecule records contained in the PubChem Compound database and provides various search and...
Integration of medicinal chemistry data from numerous public resources is an increasingly important part of academic drug discovery and translational research because it can bring a wealth of important knowledge ...
Exploring bioactive chemistry requires navigating between structures and data from a variety of text-based sources. While PubChem currently includes approximately 16 million document-extracted...
PubChem is a free and publicly available resource ... activity information. PubChem3D is an extension to PubChem containing computationally-derived three-dimensional (3-D...
Two-dimensional (2D) chemical fingerprints are widely used as binary features for the quantification of structural similarity of chemical compounds, which is an important step in similarity-based virtual scree...
PubChem provides a 3-D neighboring relationship, which ... be a 3-D neighbor. As such, PubChem employs a series of pre-filters, based ... leads one to wonder: can the existing PubChem 3-D neighboring relationship...
MetFrag has gone through algorithmic and scoring refinements. New features include the retrieval of reference, data source and patent information via ChemSpider and PubChem web services, as well as InChIKey filte...
Correctness of structures and associated metadata within public and commercial chemical databases greatly impacts drug discovery research activities such as quantitative structure–property relationships modell...
While chemical databases can be queried using the InChI string and InChIKey (IK) the latter was designed for open-web searching. It is becoming increasingly effective for this since more sources enhance crawli...
An important step in the reconstruction of a metabolic network is annotation of metabolites. Metabolites are generally annotated with various database or structure based identifiers. Metabolite annotations in ...
The absorption, distribution, metabolism, excretion, and toxicity (ADMET) of drugs plays a key role in determining which among the potential candidates are to be prioritized. In silico approaches based on mach...
The software for the IUPAC Chemical Identifier, InChI, is extraordinarily reliable. It has been tested on large databases around the world, and has proved itself to be an essential tool in the handling and integr...
In recent years, there has been a huge increase in the amount of publicly-available and proprietary information pertinent to drug discovery. However, there is a distinct lack of data mining tools available to ...
Our system uses a mixture of expertly curated grammars and dictionaries, as well as dictionaries automatically derived from public resources. We show that the heuristics developed to filter our dictionary of triv...
This article is part of a Supplement: Volume 7 Supplement 1
The discovery of both distinctive lead molecules and novel drug targets is a great challenge in drug discovery, which particularly accounts for orphan diseases. Huntington’s disease (HD) is an orphan, neurodegene...
I describe how to use the InChI canonicalisation to derive a canonical SMILES string in a straightforward way, either incorporating the InChI normalisations (Inchified SMILES) or not (Universal SMILES). This is t...
The properties of fragrance molecules in the public databases SuperScent and Flavornet were analyzed to define a “fragrance-like” (FL) property range (Heavy Atom Count ≤ 21, only C, H, O, S, (O + S) ≤ 3, Hydrogen...
The shape diversity of 16.4 million biologically relevant molecules from the PubChem Compound database and their 1.46 billion...
Despite an abundance of online databases providing access to chemical data, there is increasing demand for high-quality, structure-curated, open data to meet the various needs of the environmental sciences and co...
Chemogenomics data generally refers to the activity data of chemical compounds on an array of protein targets and represents an important source of information for building in silico...target prediction models. T...
The Erratum to this article has been published in Journal of Cheminformatics 2017 9:41
Relating chemical features to bioactivities is critical in molecular design and is used extensively in the lead discovery and optimization process. A variety of techniques from statistics, data mining and mach...
Biomedical information mining is increasingly recognized as a promising technique to accelerate drug discovery and development. Especially, integrative approaches which mine data from several (open) data sourc...
Compound structure identification is using increasingly more sophisticated computational tools, among which machine learning tools are a recent addition that quickly gains in importance. These tools, of which ...
Knowledge about the 3-dimensional structure, orientation and interaction of chemical compounds is important in many areas of science and technology. X-ray crystallography is one of the experimental techniques ...
The ChEMBL database is one of a number of public databases that contain bioactivity data on small molecule compounds curated from diverse sources. Incoming compounds are typically not standardised according to...
The chemfp project has had four main goals: (1) promote the FPS format as a text-based exchange format for dense binary cheminformatics fingerprints, (2) develop a high-performance implementation of the BitBound ...
The Correction to this article has been published in Journal of Cheminformatics 2020 12:59
This study aims at improving upon existing activity predictions methods by augmenting chemical structure fingerprints with bio-activity based fingerprints derived from high-throughput screening (HTS) data (HTSFPs...
A wide range of chemical compound databases are currently available for pharmaceutical research. To retrieve compound information, including structures, researchers can query these chemical databases using non...
Proteinogenic and non-proteinogenic amino acids, fatty acids or glycans are some of the main building blocks of nonribsosomal peptides (NRPs) and as such may give insight into the origin, biosynthesis and bioacti...
In silico analyses are increasingly being used to support mode-of-action investigations; however many such approaches do not utilise the large amounts of inactive data held in chemogenomic repositories. The objec...
Here we present Metabolic In silico Network Expansions (MINEs), an extension of known metabolite databases to include molecules that have not been observed, but are likely to occur based on known metabolites and ...
