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Identifying and assessing ligand-target binding is a core component in early drug discovery as one or more unwanted interactions may be associated with safety issues.
The maximum common property similarity (MCPhd) method is presented using descriptors as a new approach to determine the similarity between two chemical compounds or molecular graphs. This method uses the conce...
Structural information about chemical compounds is typically conveyed as 2D images of molecular structures in scientific documents. Unfortunately, these depictions are not a machine-readable representation of ...
An amendment to this paper has been published and can be accessed via the original article.
The original article was published in Journal of Cheminformatics 2019 11:76
Recently, deep learning has been successfully applied to molecular graph generation. Nevertheless, mitigating the computational complexity, which increases with the number of nodes in a graph, has been a major...
Named Entity Linking systems are a powerful aid to the manual curation of digital libraries, which is getting increasingly costly and inefficient due to the information overload. Models based on the Personaliz...
The technological advances of the past century, marked by the computer revolution and the advent of high-throughput screening technologies in drug discovery, opened the path to the computational analysis and v...
The objective of this work is to design a molecular generator capable of exploring known as well as unfamiliar areas of the chemical space. Our method must be flexible to adapt to very different problems. Ther...
This paper is a tutorial developed for the data analysis platform Galaxy. The purpose of Galaxy is to make high-throughput computational data analysis, such as molecular dynamics, a structured, reproducible an...
We address the problem of generating novel molecules with desired interaction properties as a multi-objective optimization problem. Interaction binding models are learned from binding data using graph convolut...
In computer-assisted synthesis planning (CASP) programs, providing as many chemical synthetic routes as possible is essential for considering optimal and alternative routes in a chemical reaction network. As t...
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...
Machine translation of chemical nomenclature has considerable application prospect in chemical text data processing between languages. However, rule based machine translation tools have to face significant com...
Root mean square displacement (RMSD) calculations play a fundamental role in the comparison of different conformers of the same ligand. This is particularly important in the evaluation of protein-ligand dockin...
We propose new invariant (the product of the corresponding primes for the ring size of each bond of an atom) as a simple unambiguous ring invariant of an atom that allows distinguishing symmetry classes in the...
Drug repositioning is the process of identifying novel therapeutic potentials for existing drugs and discovering therapies for untreated diseases. Drug repositioning, therefore, plays an important role in opti...
Mass spectrometry imaging (MSI) has become a mature, widespread analytical technique to perform non-targeted spatial metabolomics. However, the compounds used to promote desorption and ionization of the analyt...
In silico prediction of drug–target interactions is a critical phase in the sustainable drug development process, especially when the research focus is to capitalize on the repositioning of existing drugs. How...
Molecular fingerprints are essential cheminformatics tools for virtual screening and mapping chemical space. Among the different types of fingerprints, substructure fingerprints perform best for small molecule...
With the rise of artificial intelligence (AI) in drug discovery, de novo molecular generation provides new ways to explore chemical space. However, because de novo molecular generation methods rely on abundant...
Affinity fingerprints report the activity of small molecules across a set of assays, and thus permit to gather information about the bioactivities of structurally dissimilar compounds, where models based on ch...
Here, we introduce the ChemicalToolbox, a publicly available web server for performing cheminformatics analysis. The ChemicalToolbox provides an intuitive, graphical interface for common tools for downloading,...
An affinity fingerprint is the vector consisting of compound’s affinity or potency against the reference panel of protein targets. Here, we present the QAFFP fingerprint, 440 elements long in silico QSAR-based...
Molecular generative models trained with small sets of molecules represented as SMILES strings can generate large regions of the chemical space. Unfortunately, due to the sequential nature of SMILES strings, t...
Protein–ligand docking is an important approach for virtual screening and protein function annotation. Although many docking methods have been developed, most require a high-resolution crystal structure of the...
For kinase inhibitors, X-ray crystallography has revealed different types of binding modes. Currently, more than 2000 kinase inhibitors with known binding modes are available, which makes it possible to derive...
SYBA (SYnthetic Bayesian Accessibility) is a fragment-based method for the rapid classification of organic compounds as easy- (ES) or hard-to-synthesize (HS). It is based on a Bernoulli naïve Bayes classifier ...
Activity landscapes (ALs) are graphical representations that combine compound similarity and activity data. ALs are constructed for visualizing local and global structure–activity relationships (SARs) containe...
The development of drugs is often hampered due to off-target interactions leading to adverse effects. Therefore, computational methods to assess the selectivity of ligands are of high interest. Currently, sele...
Deep learning is developing as an important technology to perform various tasks in cheminformatics. In particular, graph convolutional neural networks (GCNs) have been reported to perform well in many types of...
The spectroscopy of diatomic molecules is an important research area in chemical physics due to its relevance in astrochemistry, combustion chemistry, and ultracold physics. However, there is currently no data...
Aromatic rings are important residues for biological interactions and appear to a large extent as part of protein–drug and protein–protein interactions. They are relevant for both protein stability and molecul...
MFsim is an open Java all-in-one rich-client computing environment for mesoscopic simulation with Jdpd as its default simulation kernel for Molecular Fragment (Dissipative Particle) Dynamics. The new environme...
Structure generators are widely used in de novo design studies and their performance substantially influences an outcome. Approaches based on the deep learning models and conventional atom-based approaches may...
Deep neural networks can directly learn from chemical structures without extensive, user-driven selection of descriptors in order to predict molecular properties/activities with high reliability. But these app...
Artificial intelligence (AI) is undergoing a revolution thanks to the breakthroughs of machine learning algorithms in computer vision, speech recognition, natural language processing and generative modelling. ...
We here present AutoGrow4, an open-source program for semi-automated computer-aided drug discovery. AutoGrow4 uses a genetic algorithm to evolve predicted ligands on demand and so is not limited to a virtual l...
Risk assessment of newly synthesised chemicals is a prerequisite for regulatory approval. In this context, in silico methods have great potential to reduce time, cost, and ultimately animal testing as they mak...
We report on a new cheminformatics enumeration technology—SIME, synthetic insight-based macrolide enumerator—a new and improved software technology. SIME can enumerate fully assembled macrolides with synthetic...
Recurrent neural networks have been widely used to generate millions of de novo molecules in defined chemical spaces. Reported deep generative models are exclusively based on LSTM and/or GRU units and frequent...
Over the last few decades, chemists have become skilled at designing compounds that avoid cytochrome P (CYP) 450 mediated metabolism. Typical screening assays are performed in liver microsomal fractions and it...
Natural products (NPs) have been the centre of attention of the scientific community in the last decencies and the interest around them continues to grow incessantly. As a consequence, in the last 20 years, th...
Ensemble learning helps improve machine learning results by combining several models and allows the production of better predictive performance compared to a single model. It also benefits and accelerates the ...
Training neural networks with small and imbalanced datasets often leads to overfitting and disregard of the minority class. For predictive toxicology, however, models with a good balance between sensitivity an...
We present SMILES-embeddings derived from the internal encoder state of a Transformer [1] model trained to canonize SMILES as a Seq2Seq problem. Using a CharNN [2] architecture upon the embeddings results in high...
Breast cancer resistance protein (BCRP/ABCG2), an ATP-binding cassette (ABC) efflux transporter, plays a critical role in multi-drug resistance (MDR) to anti-cancer drugs and drug–drug interactions. The predic...
Efficient and accurate prediction of molecular properties, such as lipophilicity and solubility, is highly desirable for rational compound design in chemical and pharmaceutical industries. To this end, we buil...
Research productivity in the pharmaceutical industry has declined significantly in recent decades, with higher costs, longer timelines, and lower success rates of drug candidates in clinical trials. This has p...
It was highlighted that the original article [1] contained an error in the last paragraph of the section ‘Structure search using SPARQL’, specifically in the radius of the used fingerprint. This Correction art...
The original article was published in Journal of Cheminformatics 2019 11:45
