Chemical similarity
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SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small molecules Open
SwissTargetPrediction is a web tool, on-line since 2014, that aims to predict the most probable protein targets of small molecules. Predictions are based on the similarity principle, through reverse screening. Here, we describe the 2019 ve…
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METLIN: A Technology Platform for Identifying Knowns and Unknowns Open
METLIN originated as a database to characterize known metabolites and has since expanded into a technology platform for the identification of known and unknown metabolites and other chemical entities. Through this effort it has become a co…
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Cheminformatics in Natural Product‐based Drug Discovery Open
This review seeks to provide a timely survey of the scope and limitations of cheminformatics methods in natural product‐based drug discovery. Following an overview of data resources of chemical, biological and structural information on nat…
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R-BIND: An Interactive Database for Exploring and Developing RNA-Targeted Chemical Probes Open
While the opportunities available for targeting RNA with small molecules have been widely appreciated, the challenges associated with achieving specific RNA recognition in biological systems have hindered progress and prevented many resear…
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A chemical–biological similarity-based grouping of complex substances as a prototype approach for evaluating chemical alternatives Open
An experimental and computational approach to categorizing UVCBs according to chemical and biological similarities.
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Large-Scale Chemical Similarity Networks for Target Profiling of Compounds Identified in Cell-Based Chemical Screens Open
Target identification is one of the most critical steps following cell-based phenotypic chemical screens aimed at identifying compounds with potential uses in cell biology and for developing novel disease therapies. Current in silico targe…
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Predicting protein targets for drug-like compounds using transcriptomics Open
An expanded chemical space is essential for improved identification of small molecules for emerging therapeutic targets. However, the identification of targets for novel compounds is biased towards the synthesis of known scaffolds that bin…
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Similarity-Based Machine Learning Model for Predicting the Metabolic Pathways of Compounds Open
Metabolic pathways refer to the continuous chemical reactions in the metabolic process in vivo. Compounds are the major participant for most metabolic pathways. It is essential to determine which compounds can constitute a metabolic pathwa…
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PLATO: A Predictive Drug Discovery Web Platform for Efficient Target Fishing and Bioactivity Profiling of Small Molecules Open
PLATO (Polypharmacology pLATform predictiOn) is an easy-to-use drug discovery web platform, which has been designed with a two-fold objective: to fish putative protein drug targets and to compute bioactivity values of small molecules. Pred…
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3D Chemical Similarity Networks for Structure-Based Target Prediction and Scaffold Hopping Open
Target identification remains a major challenge for modern drug discovery programs aimed at understanding the molecular mechanisms of drugs. Computational target prediction approaches like 2D chemical similarity searches have been widely u…
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Chemical databases: curation or integration by user-defined equivalence? Open
There is a wealth of valuable chemical information in publicly available databases for use by scientists undertaking drug discovery. However finite curation resource, limitations of chemical structure software and differences in individual…
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USR-VS: a web server for large-scale prospective virtual screening using ultrafast shape recognition techniques Open
Ligand-based Virtual Screening (VS) methods aim at identifying molecules with a similar activity profile across phenotypic and macromolecular targets to that of a query molecule used as search template. VS using 3D similarity methods have …
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Molecular Sieves for the Separation of Hydrogen Isotopes Open
Stable molecular hydrogen isotopes, D2 and T2, are both scarce and essential in several energy, industrial, and large-scale fundamental research applications. Due to the chemical similarity of these isotopes, their extraction and purificat…
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Release of 50 new, drug-like compounds and their computational target predictions for open source anti-tubercular drug discovery Open
As a follow up to the antimycobacterial screening exercise and the release of GSK´s first Tres Cantos Antimycobacterial Set (TCAMS-TB), this paper presents the results of a second antitubercular screening effort of two hundred and fifty th…
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Analysis of a large food chemical database: chemical space, diversity, and complexity Open
Background: Food chemicals are a cornerstone in the food industry. However, its chemical diversity has been explored on a limited basis, for instance, previous analysis of food-related databases were done up to 2,200 molecules. The goal of…
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MeFSAT: a curated natural product database specific to secondary metabolites of medicinal fungi Open
First dedicated manually curated resource on secondary metabolites and therapeutic uses of medicinal fungi. Cheminformatics based analysis of the chemical space of fungal natural products.
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Effectiveness of molecular fingerprints for exploring the chemical space of natural products Open
Natural products are a diverse class of compounds with promising biological properties, such as high potency and excellent selectivity. However, they have different structural motifs than typical drug-like compounds, e.g. , a wider range o…
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Bioactivity assessment of natural compounds using machine learning models trained on target similarity between drugs Open
Natural compounds constitute a rich resource of potential small molecule therapeutics. While experimental access to this resource is limited due to its vast diversity and difficulties in systematic purification, computational assessment of…
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In silico Design of Novel HIV-1 NNRTIs Based on Combined Modeling Studies of Dihydrofuro[3,4-d]pyrimidines Open
A novel series of dihydrofuro[3,4-d]pyrimidine (DHPY) analogs have recently been recognized as promising HIV-1 non-nucleoside reverse transcriptase (RT) inhibitors (NNRTIs) with potent antiviral activity. To better understand the pharmacol…
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Ranking Enzyme Structures in the PDB by Bound Ligand Similarity to Biological Substrates Open
There are numerous applications that use the structures of protein-ligand complexes from the PDB, such as 3D pharmacophore identification, virtual screening, and fragment-based drug design. The structures underlying these applications are …
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Improving Measures of Chemical Structural Similarity Using Machine Learning on Chemical–Genetic Interactions Open
A common strategy for identifying molecules likely to possess a desired biological activity is to search large databases of compounds for high structural similarity to a query molecule that demonstrates this activity, under the assumption …
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SDTRLS: Predicting Drug-Target Interactions for Complex Diseases Based on Chemical Substructures Open
It is well known that drug discovery for complex diseases via biological experiments is a time-consuming and expensive process. Alternatively, the computational methods provide a low-cost and high-efficiency way for predicting drug-target …
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Prediction of drug-likeness using graph convolutional attention network Open
Motivation The drug-likeness has been widely used as a criterion to distinguish drug-like molecules from non-drugs. Developing reliable computational methods to predict the drug-likeness of compounds is crucial to triage unpromising molecu…
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A Method for Finding Metabolic Pathways Using Atomic Group Tracking Open
A fundamental computational problem in metabolic engineering is to find pathways between compounds. Pathfinding methods using atom tracking have been widely used to find biochemically relevant pathways. However, these methods require the u…
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Similarity based enzymatic retrosynthesis Open
Using a large database of enzymatic transformations, similarity based enzymatic retrosynthesis search algorithm takes a holistic approach to enzymatic synthesis planning to yield a diverse set of single-step suggestions.
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Improved Deep Learning Based Method for Molecular Similarity Searching Using Stack of Deep Belief Networks Open
Virtual screening (VS) is a computational practice applied in drug discovery research. VS is popularly applied in a computer-based search for new lead molecules based on molecular similarity searching. In chemical databases similarity sear…
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Metabolite Structure Assignment Using In Silico NMR Techniques Open
A major challenge for metabolomic analysis is to obtain an unambiguous identification of the metabolites detected in a sample. Among metabolomics techniques, NMR spectroscopy is a sophisticated, powerful, and generally applicable spectrosc…
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CheMixNet: Mixed DNN Architectures for Predicting Chemical Properties using Multiple Molecular Representations Open
SMILES is a linear representation of chemical structures which encodes the connection table, and the stereochemistry of a molecule as a line of text with a grammar structure denoting atoms, bonds, rings and chains, and this information can…
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Machine learning-based chemical binding similarity using evolutionary relationships of target genes Open
Chemical similarity searching is a basic research tool that can be used to find small molecules which are similar in shape to known active molecules. Despite its popularity, the retrieval of local molecular features that are critical to fu…
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RxnSim: a tool to compare biochemical reactions Open
Summary : Quantitative assessment of chemical reaction similarity aids database searches, classification of reactions and identification of candidate enzymes. Most methods evaluate reaction similarity based on chemical transformation patte…