Articles

Predictive classification models and targets identification for betulin derivatives as Leishmania donovani inhibitors

Betulin derivatives have been proven effective in vitro against Leishmania donovani amastigotes, which cause visceral leishmaniasis. Identifying the molecular targets and molecular mechanisms underlying their act...

Authors: Yuezhou Zhang, Henri Xhaard and Leo Ghemtio

P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure

Ligand binding site prediction from protein structure has many applications related to elucidation of protein function and structure based drug discovery. It often represents only one step of many in complex c...

Authors: Radoslav Krivák and David Hoksza

Annotation and detection of drug effects in text for pharmacovigilance

Pharmacovigilance (PV) databases record the benefits and risks of different drugs, as a means to ensure their safe and effective use. Creating and maintaining such resources can be complex, since a particular ...

Authors: Paul Thompson, Sophia Daikou, Kenju Ueno, Riza Batista-Navarro, Jun’ichi Tsujii and Sophia Ananiadou

Chemotion-ELN part 2: adaption of an embedded Ketcher editor to advanced research applications

The Ketcher editor, available as an Open Source software package for drawing chemical structures, has been expanded to include several features that allow storage, management and application of templates, as w...

Authors: Serhii Kotov, Pierre Tremouilhac, Nicole Jung and Stefan Bräse

PubChem chemical structure standardization

PubChem is a chemical information repository, consisting of three primary databases: Substance, Compound, and BioAssay. When individual data contributors submit chemical substance descriptions to Substance, th...

Authors: Volker D. Hähnke, Sunghwan Kim and Evan E. Bolton

SPICES: a particle-based molecular structure line notation and support library for mesoscopic simulation

Simplified Particle Input ConnEction Specification (SPICES) is a particle-based molecular structure representation derived from straightforward simplifications of the atom-based SMILES line notation. It aims a...

Authors: Karina van den Broek, Mirco Daniel, Matthias Epple, Hubert Kuhn, Jonas Schaub and Achim Zielesny

HAMdb: a database of human autophagy modulators with specific pathway and disease information

Autophagy is an important homeostatic cellular recycling mechanism responsible for degrading unnecessary or dysfunctional cellular organelles and proteins in all living cells. In addition to its vital homeosta...

Authors: Ning-Ning Wang, Jie Dong, Lin Zhang, Defang Ouyang, Yan Cheng, Alex F. Chen, Ai-Ping Lu and Dong-Sheng Cao

Multi-objective de novo drug design with conditional graph generative model

Recently, deep generative models have revealed itself as a promising way of performing de novo molecule design. However, previous research has focused mainly on generating SMILES strings instead of molecular g...

Authors: Yibo Li, Liangren Zhang and Zhenming Liu

Novel pharmacological maps of protein lysine methyltransferases: key for target deorphanization

Epigenetic therapies are being investigated for the treatment of cancer, cognitive disorders, metabolic alterations and autoinmune diseases. Among the different epigenetic target families, protein lysine methy...

Authors: Obdulia Rabal, Andrea Castellar and Julen Oyarzabal

Molecular generative model based on conditional variational autoencoder for de novo molecular design

We propose a molecular generative model based on the conditional variational autoencoder for de novo molecular design. It is specialized to control multiple molecular properties simultaneously by imposing them...

Authors: Jaechang Lim, Seongok Ryu, Jin Woo Kim and Woo Youn Kim

ADMETlab: a platform for systematic ADMET evaluation based on a comprehensively collected ADMET database

Current pharmaceutical research and development (R&D) is a high-risk investment which is usually faced with some unexpected even disastrous failures in different stages of drug discovery. One main reason for R...

Authors: Jie Dong, Ning-Ning Wang, Zhi-Jiang Yao, Lin Zhang, Yan Cheng, Defang Ouyang, Ai-Ping Lu and Dong-Sheng Cao

Inferring potential small molecule–miRNA association based on triple layer heterogeneous network

Recently, many biological experiments have indicated that microRNAs (miRNAs) are a newly discovered small molecule (SM) drug targets that play an important role in the development and progression of human comp...

Authors: Jia Qu, Xing Chen, Ya-Zhou Sun, Jian-Qiang Li and Zhong Ming

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

Adverse drug reactions triggered by the common HLA-B*57:01 variant: virtual screening of DrugBank using 3D molecular docking

Idiosyncratic adverse drug reactions have been linked to a drug’s ability to bind with a human leukocyte antigen (HLA) protein. However, due to the thousands of HLA variants and limited structural data for dru...

Authors: George Van Den Driessche and Denis Fourches

3D-QSAR study of steroidal and azaheterocyclic human aromatase inhibitors using quantitative profile of protein–ligand interactions

Aromatase is a member of the cytochrome P450 superfamily responsible for a key step in the biosynthesis of estrogens. As estrogens are involved in the control of important reproduction-related processes, inclu...

Authors: Sehan Lee and Mace G. Barron

An automated framework for QSAR model building

In-silico quantitative structure–activity relationship (QSAR) models based tools are widely used to screen huge databases of compounds in order to determine the biological properties of chemical molecules base...

Authors: Samina Kausar and Andre O. Falcao

Computer-aided design of multi-target ligands at A₁R, A_2AR and PDE10A, key proteins in neurodegenerative diseases

Compounds designed to display polypharmacology may have utility in treating complex diseases, where activity at multiple targets is required to produce a clinical effect. In particular, suitable compounds may ...

Authors: Leen Kalash, Cristina Val, Jhonny Azuaje, María I. Loza, Fredrik Svensson, Azedine Zoufir, Lewis Mervin, Graham Ladds, José Brea, Robert Glen, Eddy Sotelo and Andreas Bender

Systematic exploration of multiple drug binding sites

Targets with multiple (prerequisite or allosteric) binding sites have an increasing importance in drug design. Experimental determination of atomic resolution structures of ligands weakly bound to multiple bin...

Authors: Mónika Bálint, Norbert Jeszenői, István Horváth, David van der Spoel and Csaba Hetényi

HawkRank: a new scoring function for protein–protein docking based on weighted energy terms

Deciphering the structural determinants of protein–protein interactions (PPIs) is essential to gain a deep understanding of many important biological functions in the living cells. Computational approaches for...

Authors: Ting Feng, Fu Chen, Yu Kang, Huiyong Sun, Hui Liu, Dan Li, Feng Zhu and Tingjun Hou

Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0

Network generation tools coupled with chemical reaction rules have been mainly developed for synthesis planning and more recently for metabolic engineering. Using the same core algorithm, these tools apply a s...

Authors: Mathilde Koch, Thomas Duigou, Pablo Carbonell and Jean-Loup Faulon

Can human experts predict solubility better than computers?

In this study, we design and carry out a survey, asking human experts to predict the aqueous solubility of druglike organic compounds. We investigate whether these experts, drawn largely from the pharmaceutica...

Authors: Samuel Boobier, Anne Osbourn and John B. O. Mitchell

BoBER: web interface to the base of bioisosterically exchangeable replacements

We describe a novel freely available web server Base of Bioisosterically Exchangeable Replacements (BoBER), which implements an interface to a database of bioisosteric and scaffold hopping replacements. Bioiso...

Authors: Samo Lešnik, Blaž Škrlj, Nika Eržen, Urban Bren, Stanislav Gobec, Janez Konc and Dušanka Janežič

Consensus queries in ligand-based virtual screening experiments

In ligand-based virtual screening experiments, a known active ligand is used in similarity searches to find putative active compounds for the same protein target. When there are several known active molecules,...

Authors: Francois Berenger, Oanh Vu and Jens Meiler

The CompTox Chemistry Dashboard: a community data resource for environmental chemistry

Despite an abundance of online databases providing access to chemical data, there is increasing demand for high-quality, structure-curated, open data to meet the various needs of the environmental sciences and co...

Authors: Antony J. Williams, Christopher M. Grulke, Jeff Edwards, Andrew D. McEachran, Kamel Mansouri, Nancy C. Baker, Grace Patlewicz, Imran Shah, John F. Wambaugh, Richard S. Judson and Ann M. Richard

Efficient conformational ensemble generation of protein-bound peptides

Conformation generation of protein-bound peptides is critical for the determination of protein–peptide complex structures. Despite significant progress in conformer generation of small molecules, few methods h...

Authors: Yumeng Yan, Di Zhang and Sheng-You Huang

eTOX ALLIES: an automated pipeLine for linear interaction energy-based simulations

Computational methods to predict binding affinities of small ligands toward relevant biological (off-)targets are helpful in prioritizing the screening and synthesis of new drug candidates, thereby speeding up...

Authors: Luigi Capoferri, Marc van Dijk, Ariën S. Rustenburg, Tsjerk A. Wassenaar, Derk P. Kooi, Eko A. Rifai, Nico P. E. Vermeulen and Daan P. Geerke