Research article
Self-interactions Proteins (SIPs) is important for their biological activity owing to the inherent interaction amongst their secondary structures or domains. However, due to the limitations of experimental Sel...
Journal of Cheminformatics 2017 9:47
Published on: 18 August 2017
Research article
Natural products represent a prominent source of pharmaceutically and industrially important agents. Calculating the chemical similarity of two molecules is a central task in cheminformatics, with applications...
Journal of Cheminformatics 2017 9:46
Published on: 16 August 2017
Research article
The increase of publicly available bioactivity data in recent years has fueled and catalyzed research in chemogenomics, data mining, and modeling approaches. As a direct result, over the past few years a multi...
Journal of Cheminformatics 2017 9:45
Published on: 14 August 2017
Research article
The goal of defining an applicability domain for a predictive classification model is to identify the region in chemical space where the model’s predictions are reliable. The boundary of the applicability doma...
Journal of Cheminformatics 2017 9:44
Published on: 3 August 2017
Research article
Drug design of protein kinase inhibitors is now greatly enabled by thousands of publicly available X-ray structures, extensive ligand binding data, and optimized scaffolds coming off patent. The extensive dat...
Journal of Cheminformatics 2017 9:43
Published on: 4 July 2017
Research article
In recent years, research in artificial neural networks has resurged, now under the deep-learning umbrella, and grown extremely popular. Recently reported success of DL techniques in crowd-sourced QSAR and pre...
Journal of Cheminformatics 2017 9:42
Published on: 28 June 2017
Research article
The mechanism of each chemical reaction in a metabolic network can be represented as a set of atom mappings, each of which relates an atom in a substrate metabolite to an atom of the same element in a product ...
Journal of Cheminformatics 2017 9:39
Published on: 14 June 2017
Editorial
Journal of Cheminformatics 2017 9:40
Published on: 14 June 2017
Erratum
Journal of Cheminformatics 2017 9:41
Published on: 14 June 2017
The original article was published in Journal of Cheminformatics 2017 9:17
Research article
In drug design, an efficient structure-based optimization of a ligand needs the precise knowledge of the protein–ligand interactions. In the absence of experimental information, docking programs are necessary ...
Journal of Cheminformatics 2017 9:37
Published on: 12 June 2017
Software
Analyzing files containing chemical information is at the core of cheminformatics. Each analysis may require a unique workflow. This paper describes the chemalot and chemalot_knime open source packages. Chemal...
Journal of Cheminformatics 2017 9:38
Published on: 12 June 2017
Software
In previous reports, Marrero-Ponce et al. proposed algebraic formalisms for characterizing topological (2D) and chiral (2.5D) molecular features through atom- and bond-based ToMoCoMD-CARDD (acronym for Topolo...
Journal of Cheminformatics 2017 9:35
Published on: 7 June 2017
Methodology
The concept of functional groups forms a basis of organic chemistry, medicinal chemistry, toxicity assessment, spectroscopy and also chemical nomenclature. All current software systems to identify functional g...
Journal of Cheminformatics 2017 9:36
Published on: 7 June 2017
Software
The Chemistry Development Kit (CDK) is a widely used open source cheminformatics toolkit, providing data structures to represent chemical concepts along with methods to manipulate such structures and perform ...
Journal of Cheminformatics 2017 9:33
Published on: 6 June 2017
Research article
An important aspect of chemoinformatics and material-informatics is the usage of machine learning algorithms to build Quantitative Structure Activity Relationship (QSAR) models. The RANdom SAmple Consensus (RA...
Journal of Cheminformatics 2017 9:34
Published on: 6 June 2017
Research article
In mass spectrometry-based untargeted metabolomics, rarely more than 30% of the compounds are identified. Without the true identity of these molecules it is impossible to draw conclusions about the biological ...
Journal of Cheminformatics 2017 9:32
Published on: 25 May 2017
Research article
Despite the increasingly digital nature of society there are some areas of research that remain firmly rooted in the past; in this case the laboratory notebook, the last remaining paper component of an experim...
Journal of Cheminformatics 2017 9:31
Published on: 24 May 2017
Software
CPANNatNIC is software for development of counter-propagation artificial neural network models. Besides the interface for training of a new neural network it also provides an interface for visualisation of the...
Journal of Cheminformatics 2017 9:30
Published on: 22 May 2017
Research article
Drug-like ligands obtained from protein–ligand complexes deposited in the Protein Databank were subjected to conformational searching using various force fields and solvation settings. For each ligand, the res...
Journal of Cheminformatics 2017 9:29
Published on: 15 May 2017
Software
The era of big data is influencing the way how rational drug discovery and the development of bioactive molecules is performed and versatile tools are needed to assist in molecular design workflows. Scaffold H...
Journal of Cheminformatics 2017 9:28
Published on: 11 May 2017
Software
In recent years, predictive models based on machine learning techniques have proven to be feasible and effective in drug discovery. However, to develop such a model, researchers usually have to combine multipl...
Journal of Cheminformatics 2017 9:27
Published on: 4 May 2017
Research article
Large purchasable screening libraries of small molecules afforded by commercial vendors are indispensable sources for virtual screening (VS). Selecting an optimal screening library for a specific VS campaign i...
Journal of Cheminformatics 2017 9:25
Published on: 21 April 2017
Research article
Patents are an important source of information for effective decision making in drug discovery. Encouragingly, freely accessible patent-chemistry databases are now in the public domain. However, at present the...
Journal of Cheminformatics 2017 9:26
Published on: 21 April 2017
Research article
Computational prediction of the interaction between drugs and targets is a standing challenge in the field of drug discovery. A number of rather accurate predictions were reported for various binary drug–targe...
Journal of Cheminformatics 2017 9:24
Published on: 18 April 2017
Research article
The algorithmic, large-scale use and analysis of reaction databases such as Reaxys is currently hindered by the absence of widely adopted standards for publishing reaction data in machine readable formats. Cru...
Journal of Cheminformatics 2017 9:23
Published on: 11 April 2017
