Journal of Cheminformatics

http://link.springer.com/journal/13321

List of Papers (Total 771)

osFP: a web server for predicting the oligomeric states of fluorescent proteins

Background Currently, monomeric fluorescent proteins (FP) are ideal markers for protein tagging. The prediction of oligomeric states is helpful for enhancing live biomedical imaging. Computational prediction of FP oligomeric states can accelerate the effort of protein engineering efforts of creating monomeric FPs. To the best of our knowledge, this study represents the first ...

Scaffold analysis of PubChem database as background for hierarchical scaffold-based visualization

Background Visualization of large molecular datasets is a challenging yet important topic utilised in diverse fields of chemistry ranging from material engineering to drug design. Especially in drug design, modern methods of high-throughput screening generate large amounts of molecular data that call for methods enabling their analysis. One such method is classification of ...

ChemEngine: harvesting 3D chemical structures of supplementary data from PDF files

Digital access to chemical journals resulted in a vast array of molecular information that is now available in the supplementary material files in PDF format. However, extracting this molecular information, generally from a PDF document format is a daunting task. Here we present an approach to harvest 3D molecular data from the supporting information of scientific research articles ...

Utilizing maximal frequent itemsets and social network analysis for HIV data analysis

Acquired immune deficiency syndrome is a deadly disease which is caused by human immunodeficiency virus (HIV). This virus attacks patients immune system and effects its ability to fight against diseases. Developing effective medicine requires understanding the life cycle and replication ability of the virus. HIV-1 protease enzyme is used to cleave an octamer peptide into peptides ...

Mapping the 3D structures of small molecule binding sites

Background Analysis of the 3D structures of protein–ligand binding sites can provide valuable insights for drug discovery. Binding site comparison (BSC) studies can be employed to elucidate the function of orphan proteins or to predict the potential for polypharmacology. Many previous binding site analyses only consider binding sites surrounding an experimentally observed bound ...

Programmatic conversion of crystal structures into 3D printable files using Jmol

Background Three-dimensional (3D) printed crystal structures are useful for chemistry teaching and research. Current manual methods of converting crystal structures into 3D printable files are time-consuming and tedious. To overcome this limitation, we developed a programmatic method that allows for facile conversion of thousands of crystal structures directly into 3D printable ...

Towards agile large-scale predictive modelling in drug discovery with flow-based programming design principles

Predictive modelling in drug discovery is challenging to automate as it often contains multiple analysis steps and might involve cross-validation and parameter tuning that create complex dependencies between tasks. With large-scale data or when using computationally demanding modelling methods, e-infrastructures such as high-performance or cloud computing are required, adding to ...

Prediction of reacting atoms for the major biotransformation reactions of organic xenobiotics

Background The knowledge of drug metabolite structures is essential at the early stage of drug discovery to understand the potential liabilities and risks connected with biotransformation. The determination of the site of a molecule at which a particular metabolic reaction occurs could be used as a starting point for metabolite identification. The prediction of the site of ...

A novel applicability domain technique for mapping predictive reliability across the chemical space of a QSAR: reliability-density neighbourhood

The ability to define the regions of chemical space where a predictive model can be safely used is a necessary condition to assure the reliability of new predictions. This implies that reliability must be determined across chemical space in the attempt to localize “safe” and “unsafe” regions for prediction. As a result we devised an applicability domain technique that addresses the ...

LA-iMageS: a software for elemental distribution bioimaging using LA–ICP–MS data

The spatial distribution of chemical elements in different types of samples is an important field in several research areas such as biology, paleontology or biomedicine, among others. Elemental distribution imaging by laser ablation inductively coupled plasma mass spectrometry (LA–ICP–MS) is an effective technique for qualitative and quantitative imaging due to its high spatial ...

DRABAL: novel method to mine large high-throughput screening assays using Bayesian active learning

Background Mining high-throughput screening (HTS) assays is key for enhancing decisions in the area of drug repositioning and drug discovery. However, many challenges are encountered in the process of developing suitable and accurate methods for extracting useful information from these assays. Virtual screening and a wide variety of databases, methods and solutions proposed ...

Consensus Diversity Plots: a global diversity analysis of chemical libraries

Background Measuring the structural diversity of compound databases is relevant in drug discovery and many other areas of chemistry. Since molecular diversity depends on molecular representation, comprehensive chemoinformatic analysis of the diversity of libraries uses multiple criteria. For instance, the diversity of the molecular libraries is typically evaluated employing ...

Similar compounds versus similar conformers: complementarity between PubChem 2-D and 3-D neighboring sets

Background PubChem is a public repository for biological activities of small molecules. For the efficient use of its vast amount of chemical information, PubChem performs 2-dimensional (2-D) and 3-dimensional (3-D) neighborings, which precompute “neighbor” relationships between molecules in the PubChem Compound database, using the PubChem subgraph fingerprints-based 2-D similarity ...

ClassyFire: automated chemical classification with a comprehensive, computable taxonomy

Background Scientists have long been driven by the desire to describe, organize, classify, and compare objects using taxonomies and/or ontologies. In contrast to biology, geology, and many other scientific disciplines, the world of chemistry still lacks a standardized chemical ontology or taxonomy. Several attempts at chemical classification have been made; but they have mostly ...

Filtered circular fingerprints improve either prediction or runtime performance while retaining interpretability

Background Even though circular fingerprints have been first introduced more than 50 years ago, they are still widely used for building highly predictive, state-of-the-art (Q)SAR models. Historically, these structural fragments were designed to search large molecular databases. Hence, to derive a compact representation, circular fingerprint fragments are often folded to ...

Recognizing chemicals in patents: a comparative analysis

Recently, methods for Chemical Named Entity Recognition (NER) have gained substantial interest, driven by the need for automatically analyzing todays ever growing collections of biomedical text. Chemical NER for patents is particularly essential due to the high economic importance of pharmaceutical findings. However, NER on patents has essentially been neglected by the research ...

Multi-level meta-workflows: new concept for regularly occurring tasks in quantum chemistry

Background In Quantum Chemistry, many tasks are reoccurring frequently, e.g. geometry optimizations, benchmarking series etc. Here, workflows can help to reduce the time of manual job definition and output extraction. These workflows are executed on computing infrastructures and may require large computing and data resources. Scientific workflows hide these infrastructures and the ...

NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges

Background The concept of partial atomic charges was first applied in physical and organic chemistry and was later also adopted in computational chemistry, bioinformatics and chemoinformatics. The electronegativity equalization method (EEM) is the most frequently used approach for calculating partial atomic charges. EEM is fast and its accuracy is comparable to the quantum ...

Benchmark of four popular virtual screening programs: construction of the active/decoy dataset remains a major determinant of measured performance

Background In a structure-based virtual screening, the choice of the docking program is essential for the success of a hit identification. Benchmarks are meant to help in guiding this choice, especially when undertaken on a large variety of protein targets. Here, the performance of four popular virtual screening programs, Gold, Glide, Surflex and FlexX, is compared using the ...

SciData: a data model and ontology for semantic representation of scientific data

With the move toward global, Internet enabled science there is an inherent need to capture, store, aggregate and search scientific data across a large corpus of heterogeneous data silos. As a result, standards development is needed to create an infrastructure capable of representing the diverse nature of scientific data. This paper describes a fundamental data model for scientific ...

Improving chemical disease relation extraction with rich features and weakly labeled data

Background Due to the importance of identifying relations between chemicals and diseases for new drug discovery and improving chemical safety, there has been a growing interest in developing automatic relation extraction systems for capturing these relations from the rich and rapid-growing biomedical literature. In this work we aim to build on current advances in named entity ...

Evolution of DFT studies in view of a scientometric perspective

Background This bibliometric study aims to analyze the publications in which density functional theory (DFT) plays a major role. The bibliometric analysis is performed on the full publication volume of 114,138 publications as well as sub-sets defined in terms of six different types of compounds and nine different research topics. Also, a compound analysis is presented that shows ...

Computational methods for prediction of in vitro effects of new chemical structures

Background 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 profiles. In recent years, in silico prediction methods received great attention in an attempt to reduce animal experiments for the evaluation of various toxicological ...

Jmol SMILES and Jmol SMARTS: specifications and applications

Background 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 implemented in both Java and JavaScript. Over the past 10 years, from 2007 to 2016, work on Jmol has included the development of dialects of SMILES and SMARTS that ...

An ensemble model of QSAR tools for regulatory risk assessment

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 for chemical risk assessment for protection of human and environmental health, which makes them interesting to regulators, especially in the absence of experimental data. For ...