Articles

Putting hands to rest: efficient deep CNN-RNN architecture for chemical named entity recognition with no hand-crafted rules

Chemical named entity recognition (NER) is an active field of research in biomedical natural language processing. To facilitate the development of new and superior chemical NER systems, BioCreative released th...

Authors: Ilia Korvigo, Maxim Holmatov, Anatolii Zaikovskii and Mikhail Skoblov

Sachem: a chemical cartridge for high-performance substructure search

Structure search is one of the valuable capabilities of small-molecule databases. Fingerprint-based screening methods are usually employed to enhance the search performance by reducing the number of calls to t...

Authors: Miroslav Kratochvíl, Jiří Vondrášek and Jakub Galgonek

Effect of missing data on multitask prediction methods

There has been a growing interest in multitask prediction in chemoinformatics, helped by the increasing use of deep neural networks in this field. This technique is applied to multitarget data sets, where comp...

Authors: Antonio de la Vega de León, Beining Chen and Valerie J. Gillet

RepTB: a gene ontology based drug repurposing approach for tuberculosis

Tuberculosis (TB) is the world’s leading infectious killer with 1.8 million deaths in 2015 as reported by WHO. It is therefore imperative that alternate routes of identification of novel anti-TB compounds are ...

Authors: Anurag Passi, Neeraj Kumar Rajput, David J. Wild and Anshu Bhardwaj

Jdpd: an open java simulation kernel for molecular fragment dissipative particle dynamics

Jdpd is an open Java simulation kernel for Molecular Fragment Dissipative Particle Dynamics with parallelizable force calculation, efficient caching options and fast property calculations. It is characterized ...

Authors: Karina van den Broek, Hubert Kuhn and Achim Zielesny

Using SMILES strings for the description of chemical connectivity in the Crystallography Open Database

Computer descriptions of chemical molecular connectivity are necessary for searching chemical databases and for predicting chemical properties from molecular structure. In this article, the ongoing work to des...

Authors: Miguel Quirós, Saulius Gražulis, Saulė Girdzijauskaitė, Andrius Merkys and Antanas Vaitkus

International chemical identifier for reactions (RInChI)

The Reaction InChI (RInChI) extends the idea of the InChI, which provides a unique descriptor of molecular structures, towards reactions. Prototype versions of the RInChI have been available since 2011. The fi...

Authors: Guenter Grethe, Gerd Blanke, Hans Kraut and Jonathan M. Goodman

Finding the molecular scaffold of nuclear receptor inhibitors through high-throughput screening based on proteochemometric modelling

Nuclear receptors (NR) are a class of proteins that are responsible for sensing steroid and thyroid hormones and certain other molecules. In that case, NR have the ability to regulate the expression of specifi...

Authors: Tianyi Qiu, Dingfeng Wu, Jingxuan Qiu and Zhiwei Cao

KRDS: a web server for evaluating drug resistance mutations in kinases by molecular docking

Kinases are major targets of anti-cancer therapies owing to their importance in signaling processes that regulate cell growth and proliferation. However, drug resistance has emerged as a major obstacle to canc...

Authors: Aeri Lee, Seungpyo Hong and Dongsup Kim

Finding the K best synthesis plans

In synthesis planning, the goal is to synthesize a target molecule from available starting materials, possibly optimizing costs such as price or environmental impact of the process. Current algorithmic approac...

Authors: Rolf Fagerberg, Christoph Flamm, Rojin Kianian, Daniel Merkle and Peter F. Stadler

A confidence predictor for logD using conformal regression and a support-vector machine

Lipophilicity is a major determinant of ADMET properties and overall suitability of drug candidates. We have developed large-scale models to predict water–octanol distribution coefficient (logD) for chemical c...

Authors: Maris Lapins, Staffan Arvidsson, Samuel Lampa, Arvid Berg, Wesley Schaal, Jonathan Alvarsson and Ola Spjuth

The dye-sensitized solar cell database

Dye-sensitized solar cells (DSSCs) have garnered a lot of attention in recent years. The solar energy to power conversion efficiency of a DSSC is influenced by various components of the cell such as the dye, e...

Authors: Vishwesh Venkatraman, Rajesh Raju, Solon P. Oikonomopoulos and Bjørn K. Alsberg

PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions

With the increasing development of biotechnology and informatics technology, publicly available data in chemistry and biology are undergoing explosive growth. Such wealthy information in these data needs to b...

Authors: Jie Dong, Zhi-Jiang Yao, Lin Zhang, Feijun Luo, Qinlu Lin, Ai-Ping Lu, Alex F. Chen and Dong-Sheng Cao

A novel interaction fingerprint derived from per atom score contributions: exhaustive evaluation of interaction fingerprint performance in docking based virtual screening

Protein ligand interaction fingerprints are a powerful approach for the analysis and assessment of docking poses to improve docking performance in virtual screening. In this study, a novel interaction fingerpr...

Authors: Julia B. Jasper, Lina Humbeck, Tobias Brinkjost and Oliver Koch

Comment on “The power metric: a new statistically robust enrichment-type metric for virtual screening applications with early recovery capability”

Authors: M. Šícho, M. Voršilák and D. Svozil

Reply to the comment made by Šicho, Vorśilák and Svozil on ‘The Power metric: a new statistically robust enrichment-type metric for virtual screening applications with early recovery capability’

Authors: Hans De Winter and Julio Cesar Dias Lopes

HIVprotI: an integrated web based platform for prediction and design of HIV proteins inhibitors

A number of anti-retroviral drugs are being used for treating Human Immunodeficiency Virus (HIV) infection. Due to emergence of drug resistant strains, there is a constant quest to discover more effective anti...

Authors: Abid Qureshi, Akanksha Rajput, Gazaldeep Kaur and Manoj Kumar

Automated reaction database and reaction network analysis: extraction of reaction templates using cheminformatics

Both the automated generation of reaction networks and the automated prediction of synthetic trees require, in one way or another, the definition of possible transformations a molecule can undergo. One way of ...

Authors: Pieter P. Plehiers, Guy B. Marin, Christian V. Stevens and Kevin M. Van Geem

OPERA models for predicting physicochemical properties and environmental fate endpoints

The collection of chemical structure information and associated experimental data for quantitative structure–activity/property relationship (QSAR/QSPR) modeling is facilitated by an increasing number of public...

Authors: Kamel Mansouri, Chris M. Grulke, Richard S. Judson and Antony J. Williams

Spectrophores as one-dimensional descriptors calculated from three-dimensional atomic properties: applications ranging from scaffold hopping to multi-target virtual screening

Spectrophores are novel descriptors that are calculated from the three-dimensional atomic properties of molecules. In our current implementation, the atomic properties that were used to calculate spectrophores...

Authors: Rafaela Gladysz, Fabio Mendes Dos Santos, Wilfried Langenaeker, Gert Thijs, Koen Augustyns and Hans De Winter

Efficient iterative virtual screening with Apache Spark and conformal prediction

Docking and scoring large libraries of ligands against target proteins forms the basis of structure-based virtual screening. The problem is trivially parallelizable, and calculations are generally carried out ...

Authors: Laeeq Ahmed, Valentin Georgiev, Marco Capuccini, Salman Toor, Wesley Schaal, Erwin Laure and Ola Spjuth

Maximizing gain in high-throughput screening using conformal prediction

Iterative screening has emerged as a promising approach to increase the efficiency of screening campaigns compared to traditional high throughput approaches. By learning from a subset of the compound library, ...

Authors: Fredrik Svensson, Avid M. Afzal, Ulf Norinder and Andreas Bender

Two inhibitors of yeast plasma membrane ATPase 1 (ScPma1p): toward the development of novel antifungal therapies

Given that many antifungal medications are susceptible to evolved resistance, there is a need for novel drugs with unique mechanisms of action. Inhibiting the essential proton pump Pma1p, a P-type ATPase, is a...

Authors: Sabine Ottilie, Gregory M. Goldgof, Andrea L. Cheung, Jennifer L. Walker, Edgar Vigil, Kenneth E. Allen, Yevgeniya Antonova-Koch, Carolyn W. Slayman, Yo Suzuki and Jacob D. Durrant

Key features and updates for Origin 2018

OriginLab’s newest version update to Origin and OriginPro includes ease-of-use features, like Origin Central updates and creation of an App Center, as well as larger changes like the addition of Unicode charac...

Authors: James G. Moberly, Matthew T. Bernards and Kristopher V. Waynant

Mordred: a molecular descriptor calculator

Molecular descriptors are widely employed to present molecular characteristics in cheminformatics. Various molecular-descriptor-calculation software programs have been developed. However, users of those progra...

Authors: Hirotomo Moriwaki, Yu-Shi Tian, Norihito Kawashita and Tatsuya Takagi