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With a constant increase in the number of new chemicals synthesized every year, it becomes important to employ the most reliable and fast in silico screening methods to predict their safety and activity profil...
SMILES and SMARTS are two well-defined structure matching languages that have gained wide use in cheminformatics. Jmol is a widely used open-source molecular visualization and analysis tool written in Java and...
This communication deals with the scientific problem of evaluating the similarity between two chemical systems, each described by a finite discrete set of elements/members, which are in turn p-dimensional vectors...
Quantitative structure activity relationships (QSARs) are theoretical models that relate a quantitative measure of chemical structure to a physical property or a biological effect. QSAR predictions can be used...
Xenobiotic metabolism is an active research topic but the limited amount of openly available high-quality biotransformation data constrains predictive modeling. Current database often default to commonly avail...
Ligand-based virtual screening of large small-molecule databases is an important step in the early stages of drug development. It is based on the similarity principle and is used to reduce the chemical space o...
Receiver operating characteristics (ROC) curve with the calculation of area under curve (AUC) is a useful tool to evaluate the performance of biomedical and chemoinformatics data. For example, in virtual drug...
Liquid chromatography-high resolution mass spectrometry (LC-MS) has emerged as one of the most widely used platforms for untargeted metabolomics due to its unparalleled sensitivity and metabolite coverage. Des...
Nuclear receptors (NRs) constitute an important class of therapeutic targets. We evaluated the performance of 3D structure-based and ligand-based pharmacophore models in predicting the pharmacological profile ...
We have developed a new platform-independent web-based molecular viewer using JavaScript and WebGL. The molecular viewer, Molmil, has been integrated into several services offered by Protein Data Bank Japan an...
Highly chemically similar drugs usually possess similar biological activities, but sometimes, small changes in chemistry can result in a large difference in biological effects. Chemically similar drug pairs th...
Ionic liquids (ILs) found a variety of applications in today’s chemistry. Since their properties depend on the ions constituting particular ionic liquid, it is possible to synthetize IL with desired specificat...
The increasing size of datasets in drug discovery makes it challenging to build robust and accurate predictive models within a reasonable amount of time. In order to investigate the effect of dataset sizes on ...
Protein-binding sites prediction lays a foundation for functional annotation of protein and structure-based drug design. As the number of available protein structures increases, structural alignment based algo...
As one of the largest publicly accessible databases for hosting chemical structures and biological activities, PubChem has been processing bioassay submissions from the community since 2004. With the increase...
The concept of molecular similarity is one of the central ideas in cheminformatics, despite the fact that it is ill-defined and rather difficult to assess objectively. Here we propose a practical definition of...
Drug-target identification is crucial to discover novel applications for existing drugs and provide more insights about mechanisms of biological actions, such as adverse drug effects (ADEs). Computational meth...
More and more evidences from network biology indicate that most cellular components exert their functions through interactions with other cellular components, such as proteins, DNAs, RNAs and small molecules. ...
The disposition of a pharmaceutical compound within an organism, i.e. its Absorption, Distribution, Metabolism, Excretion, Toxicity (ADMET) properties and adverse effects, critically affects late stage failur...
PubChem is an open archive consisting of a set of three primary public databases (BioAssay, Compound, and Substance). It contains information on a broad range of chemical entities, including small molecules, l...
In recent years, the Resource Description Framework (RDF) and the SPARQL query language have become more widely used in the area of cheminformatics and bioinformatics databases. These technologies allow better...
It is now widely recognized that there is an urgent need for new antibacterial drugs, with novel mechanisms of action, to combat the rise of multi-drug resistant bacteria. However, few new compounds are reachi...
Bioassay data analysis continues to be an essential, routine, yet challenging task in modern drug discovery and chemical biology research. The challenge is to infer reliable knowledge from big and noisy data. ...
The original article was published in Journal of Cheminformatics 2016 8:16
Halogen bonding has recently come to play as a target for lead optimization in rational drug design. However, most docking program don’t account for halogen bonding in their scoring functions and are not able ...
We present “Ask Ernö”, a self-learning system for the automatic analysis of NMR spectra, consisting of integrated chemical shift assignment and prediction tools. The output of the automatic assignment component i...
Similarly to the periodic table for elements, chemical space offers an organizing principle for representing the diversity of organic molecules, usually in the form of multi-dimensional property spaces that ar...
Non-covalent interactions (NCIs) play critical roles in supramolecular chemistries; however, they are difficult to measure. Currently, reliable computational methods are being pursued to meet this challenge, ...
Small molecules are information carriers that make cells aware of external changes and couple internal metabolic and signalling pathway systems with each other. In some specific physiological status, natural o...
This study seeks to develop, test and assess a methodology for automatic extraction of a complete set of ‘term-like phrases’ and to create a terminology spectrum from a collection of natural language PDF docum...
This article is part of a Supplement: Volume 8 Supplement 1
To protect the health of human and environment, the European Union implemented the REACH regulation for chemical substances. REACH is an acronym for Registration, Evaluation, Authorization, and Restriction of ...
In silico target prediction of compounds plays an important role in drug discovery. The chemical similarity ensemble approach (SEA) is a promising method, which has been successfully applied in many drug-relat...
Since the structure of proteins is more conserved than the sequence, the identification of conserved three-dimensional (3D) patterns among a set of proteins, can be important for protein function prediction, p...
Disordered compounds are crucially important for fundamental science and industrial applications. Yet most available methods to explore solid-state material properties require ideal periodicity, which, strictl...
Complex network theory based methods and the emergence of “Big Data” have reshaped the terrain of investigating structure-activity relationships of molecules. This change gave rise to new methods which need to...
The Erratum to this article has been published in Journal of Cheminformatics 2016 8:28
Identification of novel drug–target interactions (DTIs) is important for drug discovery. Experimental determination of such DTIs is costly and time consuming, hence it necessitates the development of efficient...
Due to exorbitant costs of high-throughput screening, many drug discovery projects commonly employ inexpensive virtual screening to support experimental efforts. However, the vast majority of compounds in wide...
Assessing compound toxicity at early stages of the drug discovery process is a crucial task to dismiss drug candidates likely to fail in clinical trials. Screening drug candidates against structural alerts, i....
In-silico methods are an integral part of modern drug discovery paradigm. Virtual screening, an in-silico method, is used to refine data models and reduce the chemical space on which w...
ChEBI is a database and ontology of chemical entities of biological interest. It is widely used as a source of identifiers to facilitate unambiguous reference to chemical entities within biological models, dat...
Recently, novel 3D alignment-free molecular descriptors (also known as QuBiLS-MIDAS) based on two-linear, three-linear and four-linear algebraic forms have been introduced. These descriptors codify chemical in...
The way that we recall information is dependent upon both the knowledge in our memories and the conditions under which we recall the information. Electronic Laboratory Notebooks can provide a structured interf...
The testing of theoretical models with experimental data is an integral part of the scientific method, and a logical place to search for new ways of stimulating scientific productivity. Often experiment/theory...
The human ATP binding cassette transporters Breast Cancer Resistance Protein (BCRP) and Multidrug Resistance Protein 1 (P-gp) are co-expressed in many tissues and barriers, especially at the blood–brain barrie...
Determination of acute toxicity, expressed as median lethal dose (LD50), is one of the most important steps in drug discovery pipeline. Because in vivo assays for oral acute toxicity in mammals are time-consumin...
Untargeted metabolomics commonly uses liquid chromatography mass spectrometry to measure abundances of metabolites; subsequent tandem mass spectrometry is used to derive information about individual compounds....
The in silico fragmenter MetFrag, launched in 2010, was one of the first approaches combining compound database searching and fragmentation prediction for small molecule identification from tandem mass spectromet...
Hierarchical cluster analysis (HCA) is a widely used classificatory technique in many areas of scientific knowledge. Applications usually yield a dendrogram from an HCA run over a given data set, using a group...
Melting point (MP) is an important property in regards to the solubility of chemical compounds. Its prediction from chemical structure remains a highly challenging task for quantitative structure–activity rel...
