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Journal of Cheminformatics

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https://www.readbyqxmd.com/read/28203291/the-power-metric-a-new-statistically-robust-enrichment-type-metric-for-virtual-screening-applications-with-early-recovery-capability
#1
Julio Cesar Dias Lopes, Fábio Mendes Dos Santos, Andrelly Martins-José, Koen Augustyns, Hans De Winter
A new metric for the evaluation of model performance in the field of virtual screening and quantitative structure-activity relationship applications is described. This metric has been termed the power metric and is defined as the fraction of the true positive rate divided by the sum of the true positive and false positive rates, for a given cutoff threshold. The performance of this metric is compared with alternative metrics such as the enrichment factor, the relative enrichment factor, the receiver operating curve enrichment factor, the correct classification rate, Matthews correlation coefficient and Cohen's kappa coefficient...
2017: Journal of Cheminformatics
https://www.readbyqxmd.com/read/28203290/mapping-and-classifying-molecules-from-a-high-throughput-structural-database
#2
Sandip De, Felix Musil, Teresa Ingram, Carsten Baldauf, Michele Ceriotti
High-throughput computational materials design promises to greatly accelerate the process of discovering new materials and compounds, and of optimizing their properties. The large databases of structures and properties that result from computational searches, as well as the agglomeration of data of heterogeneous provenance leads to considerable challenges when it comes to navigating the database, representing its structure at a glance, understanding structure-property relations, eliminating duplicates and identifying inconsistencies...
2017: Journal of Cheminformatics
https://www.readbyqxmd.com/read/28194231/skinsensdb-a-curated-database-for-skin-sensitization-assays
#3
Chia-Chi Wang, Ying-Chi Lin, Shan-Shan Wang, Chieh Shih, Yi-Hui Lin, Chun-Wei Tung
Skin sensitization is an important toxicological endpoint for chemical hazard determination and safety assessment. Prediction of chemical skin sensitizer had traditionally relied on data from rodent models. The development of the adverse outcome pathway (AOP) and associated alternative in vitro assays have reshaped the assessment of skin sensitizers. The integration of multiple assays as key events in the AOP has been shown to have improved prediction performance. Current computational models to predict skin sensitization mainly based on in vivo assays without incorporating alternative in vitro assays...
2017: Journal of Cheminformatics
https://www.readbyqxmd.com/read/28184255/a-metadata-driven-approach-to-data-repository-design
#4
Matthew J Harvey, Andrew McLean, Henry S Rzepa
The design and use of a metadata-driven data repository for research data management is described. Metadata is collected automatically during the submission process whenever possible and is registered with DataCite in accordance with their current metadata schema, in exchange for a persistent digital object identifier. Two examples of data preview are illustrated, including the demonstration of a method for integration with commercial software that confers rich domain-specific data analytics without introducing customisation into the repository itself...
2017: Journal of Cheminformatics
https://www.readbyqxmd.com/read/28184254/npcare-database-of-natural-products-and-fractional-extracts-for-cancer-regulation
#5
Hwanho Choi, Sun Young Cho, Ho Jeong Pak, Youngsoo Kim, Jung-Yun Choi, Yoon Jae Lee, Byung Hee Gong, Yeon Seok Kang, Taehoon Han, Geunbae Choi, Yeeun Cho, Soomin Lee, Dekwoo Ryoo, Hwangseo Park
BACKGROUND: Natural products have increasingly attracted much attention as a valuable resource for the development of anticancer medicines due to the structural novelty and good bioavailability. This necessitates a comprehensive database for the natural products and the fractional extracts whose anticancer activities have been verified. DESCRIPTION: NPCARE (http://silver.sejong.ac.kr/npcare) is a publicly accessible online database of natural products and fractional extracts for cancer regulation...
2017: Journal of Cheminformatics
https://www.readbyqxmd.com/read/28123452/s2rsldb-a-comprehensive-manually-curated-internet-accessible-database-of-the-sigma-2-receptor-selective-ligands
#6
Giovanni Nastasi, Carla Miceli, Valeria Pittalà, Maria N Modica, Orazio Prezzavento, Giuseppe Romeo, Antonio Rescifina, Agostino Marrazzo, Emanuele Amata
BACKGROUND: Sigma (σ) receptors are accepted as a particular receptor class consisting of two subtypes: sigma-1 (σ1) and sigma-2 (σ2). The two receptor subtypes have specific drug actions, pharmacological profiles and molecular characteristics. The σ2 receptor is overexpressed in several tumor cell lines, and its ligands are currently under investigation for their role in tumor diagnosis and treatment. The σ2 receptor structure has not been disclosed, and researchers rely on σ2 receptor radioligand binding assay to understand the receptor's pharmacological behavior and design new lead compounds...
2017: Journal of Cheminformatics
https://www.readbyqxmd.com/read/28090217/scaffold-analysis-of-pubchem-database-as-background-for-hierarchical-scaffold-based-visualization
#7
Jakub Velkoborsky, David Hoksza
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 compounds based on their molecular scaffolds, a concept widely used by medicinal chemists to group molecules of similar properties...
2016: Journal of Cheminformatics
https://www.readbyqxmd.com/read/28090216/chemengine-harvesting-3d-chemical-structures-of-supplementary-data-from-pdf-files
#8
Muthukumarasamy Karthikeyan, Renu Vyas
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 that are normally available from publisher's resources. In order to demonstrate the feasibility of extracting truly computable molecules from PDF file formats in a fast and efficient manner, we have developed a Java based application, namely ChemEngine...
2016: Journal of Cheminformatics
https://www.readbyqxmd.com/read/28053671/osfp-a-web-server-for-predicting-the-oligomeric-states-of-fluorescent-proteins
#9
Saw Simeon, Watshara Shoombuatong, Nuttapat Anuwongcharoen, Likit Preeyanon, Virapong Prachayasittikul, Jarl E S Wikberg, Chanin Nantasenamat
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 computational model for predicting and analyzing FP oligomerization directly from the amino acid sequence. RESULTS: After data curation, an exhaustive data set consisting of 397 non-redundant FP oligomeric states was compiled from the literature...
2016: Journal of Cheminformatics
https://www.readbyqxmd.com/read/27994650/prediction-of-reacting-atoms-for-the-major-biotransformation-reactions-of-organic-xenobiotics
#10
Anastasia V Rudik, Alexander V Dmitriev, Alexey A Lagunin, Dmitry A Filimonov, Vladimir V Poroikov
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 metabolism does not always correspond to the particular atom that is modified by the enzyme but rather is often associated with a group of atoms...
2016: Journal of Cheminformatics
https://www.readbyqxmd.com/read/27942268/towards-agile-large-scale-predictive-modelling-in-drug-discovery-with-flow-based-programming-design-principles
#11
Samuel Lampa, Jonathan Alvarsson, Ola Spjuth
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 the existing challenges of fault-tolerant automation. Workflow management systems can aid in many of these challenges, but the currently available systems are lacking in the functionality needed to enable agile and flexible predictive modelling...
2016: Journal of Cheminformatics
https://www.readbyqxmd.com/read/27933103/programmatic-conversion-of-crystal-structures-into-3d-printable-files-using-jmol
#12
Vincent F Scalfani, Antony J Williams, Valery Tkachenko, Karen Karapetyan, Alexey Pshenichnov, Robert M Hanson, Jahred M Liddie, Jason E Bara
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 files. RESULTS: A collection of over 30,000 crystal structures in crystallographic information file (CIF) format from the Crystallography Open Database (COD) were programmatically converted into 3D printable files (VRML format) using Jmol scripting...
2016: Journal of Cheminformatics
https://www.readbyqxmd.com/read/27917244/la-images-a-software-for-elemental-distribution-bioimaging-using-la-icp-ms-data
#13
Hugo López-Fernández, Gustavo de S Pessôa, Marco A Z Arruda, José L Capelo-Martínez, Florentino Fdez-Riverola, Daniel Glez-Peña, Miguel Reboiro-Jato
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 resolution and sensitivity. By applying this technique, vast amounts of raw data are generated to obtain high-quality images, essentially making the use of specific LA-ICP-MS imaging software that can process such data absolutely mandatory...
2016: Journal of Cheminformatics
https://www.readbyqxmd.com/read/27895719/drabal-novel-method-to-mine-large-high-throughput-screening-assays-using-bayesian-active-learning
#14
Othman Soufan, Wail Ba-Alawi, Moataz Afeef, Magbubah Essack, Panos Kalnis, Vladimir B Bajic
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 to-date, did not completely overcome these challenges. This study is based on a multi-label classification (MLC) technique for modeling correlations between several HTS assays, meaning that a single prediction represents a subset of assigned correlated labels instead of one label...
2016: Journal of Cheminformatics
https://www.readbyqxmd.com/read/27895718/consensus-diversity-plots-a-global-diversity-analysis-of-chemical-libraries
#15
Mariana González-Medina, Fernando D Prieto-Martínez, John R Owen, José L Medina-Franco
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 molecular scaffolds, structural fingerprints, and physicochemical properties. However, the assessment with each criterion is analyzed independently and it is not straightforward to provide an evaluation of the "global diversity"...
2016: Journal of Cheminformatics
https://www.readbyqxmd.com/read/27872662/similar-compounds-versus-similar-conformers-complementarity-between-pubchem-2-d-and-3-d-neighboring-sets
#16
Sunghwan Kim, Evan E Bolton, Stephen H Bryant
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 and the Gaussian-shape overlay-based 3-D similarity, respectively. These neighborings allow PubChem to provide the user with immediate access to the list of 2-D and 3-D neighbors (also called "Similar Compounds" and "Similar Conformers", respectively) for each compound in PubChem...
2016: Journal of Cheminformatics
https://www.readbyqxmd.com/read/27867422/classyfire-automated-chemical-classification-with-a-comprehensive-computable-taxonomy
#17
Yannick Djoumbou Feunang, Roman Eisner, Craig Knox, Leonid Chepelev, Janna Hastings, Gareth Owen, Eoin Fahy, Christoph Steinbeck, Shankar Subramanian, Evan Bolton, Russell Greiner, David S Wishart
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 been limited to either manual, or semi-automated proof-of-principle applications. This is regrettable as comprehensive chemical classification and description tools could not only improve our understanding of chemistry but also improve the linkage between chemistry and many other fields...
2016: Journal of Cheminformatics
https://www.readbyqxmd.com/read/27853484/filtered-circular-fingerprints-improve-either-prediction-or-runtime-performance-while-retaining-interpretability
#18
Martin Gütlein, Stefan Kramer
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 comparatively short bit-strings. However, folding fingerprints introduces bit collisions, and therefore adds noise to the encoded structural information and removes its interpretability...
2016: Journal of Cheminformatics
https://www.readbyqxmd.com/read/27843493/recognizing-chemicals-in-patents-a-comparative-analysis
#19
Maryam Habibi, David Luis Wiegandt, Florian Schmedding, Ulf Leser
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 community for long, mostly because of the lack of enough annotated corpora. A recent international competition specifically targeted this task, but evaluated tools only on gold standard patent abstracts instead of full patents; furthermore, results from such competitions are often difficult to extrapolate to real-life settings due to the relatively high homogeneity of training and test data...
2016: Journal of Cheminformatics
https://www.readbyqxmd.com/read/27818709/multi-level-meta-workflows-new-concept-for-regularly-occurring-tasks-in-quantum-chemistry
#20
Junaid Arshad, Alexander Hoffmann, Sandra Gesing, Richard Grunzke, Jens Krüger, Tamas Kiss, Sonja Herres-Pawlis, Gabor Terstyanszky
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 resources needed to run them. It requires significant efforts and specific expertise to design, implement and test these workflows...
2016: Journal of Cheminformatics
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