Articles

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

An efficient computer-aided structural elucidation strategy for mixtures using an iterative dynamic programming algorithm

The identification of chemical structures in natural product mixtures is an important task in drug discovery but is still a challenging problem, as structural elucidation is a time-consuming process and is li...

Authors: Bo-Han Su, Meng-Yu Shen, Yeu-Chern Harn, San-Yuan Wang, Alioune Schurz, Chieh Lin, Olivia A. Lin and Yufeng J. Tseng

A posteriori metadata from automated provenance tracking: integration of AiiDA and TCOD

In order to make results of computational scientific research findable, accessible, interoperable and re-usable, it is necessary to decorate them with standardised metadata. However, there are a number of tech...

Authors: Andrius Merkys, Nicolas Mounet, Andrea Cepellotti, Nicola Marzari, Saulius Gražulis and Giovanni Pizzi

Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application

An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers an interact...

Authors: Marcus D. Hanwell, Wibe A. de Jong and Christopher J. Harris

Chemotion ELN: an Open Source electronic lab notebook for chemists in academia

The development of an electronic lab notebook (ELN) for researchers working in the field of chemical sciences is presented. The web based application is available as an Open Source software that offers modern ...

Authors: Pierre Tremouilhac, An Nguyen, Yu-Chieh Huang, Serhii Kotov, Dominic Sebastian Lütjohann, Florian Hübsch, Nicole Jung and Stefan Bräse

Erratum to: The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

Authors: Egon L. Willighagen, John W. Mayfield, Jonathan Alvarsson, Arvid Berg, Lars Carlsson, Nina Jeliazkova, Stefan Kuhn, Tomáš Pluskal, Miquel Rojas-Chertó, Ola Spjuth, Gilleain Torrance, Chris T. Evelo, Rajarshi Guha and Christoph Steinbeck

Scoria: a Python module for manipulating 3D molecular data

Third-party packages have transformed the Python programming language into a powerful computational-biology tool. Package installation is easy for experienced users, but novices sometimes struggle with depende...

Authors: Patrick Ropp, Aaron Friedman and Jacob D. Durrant

A review of parameters and heuristics for guiding metabolic pathfinding

Recent developments in metabolic engineering have led to the successful biosynthesis of valuable products, such as the precursor of the antimalarial compound, artemisinin, and opioid precursor, thebaine. Synth...

Authors: Sarah M. Kim, Matthew I. Peña, Mark Moll, George N. Bennett and Lydia E. Kavraki

G.A.M.E.: GPU-accelerated mixture elucidator

GPU acceleration is useful in solving complex chemical information problems. Identifying unknown structures from the mass spectra of natural product mixtures has been a desirable yet unresolved issue in metabo...

Authors: Alioune Schurz, Bo-Han Su, Yi-Shu Tu, Tony Tsung-Yu Lu, Olivia A. Lin and Yufeng J. Tseng

Beware of ligand efficiency (LE): understanding LE data in modeling structure-activity and structure-economy relationships

On the one hand, ligand efficiency (LE) and the binding efficiency index (BEI), which are binding properties (B) averaged versus the heavy atom count (HAC: LE) or molecular weight (MW: BEI), have recently been...

Authors: Jaroslaw Polanski, Aleksandra Tkocz and Urszula Kucia

Molecular de-novo design through deep reinforcement learning

This work introduces a method to tune a sequence-based generative model for molecular de novo design that through augmented episodic likelihood can learn to generate structures with certain specified desirable...

Authors: Marcus Olivecrona, Thomas Blaschke, Ola Engkvist and Hongming Chen

Computational methods using weighed-extreme learning machine to predict protein self-interactions with protein evolutionary information

Self-interactions Proteins (SIPs) is important for their biological activity owing to the inherent interaction amongst their secondary structures or domains. However, due to the limitations of experimental Sel...

Authors: Ji-Yong An, Lei Zhang, Yong Zhou, Yu-Jun Zhao and Da-Fu Wang

Comparative analysis of chemical similarity methods for modular natural products with a hypothetical structure enumeration algorithm

Natural products represent a prominent source of pharmaceutically and industrially important agents. Calculating the chemical similarity of two molecules is a central task in cheminformatics, with applications...

Authors: Michael A. Skinnider, Chris A. Dejong, Brian C. Franczak, Paul D. McNicholas and Nathan A. Magarvey

Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set

The increase of publicly available bioactivity data in recent years has fueled and catalyzed research in chemogenomics, data mining, and modeling approaches. As a direct result, over the past few years a multi...

Authors: Eelke B. Lenselink, Niels ten Dijke, Brandon Bongers, George Papadatos, Herman W. T. van Vlijmen, Wojtek Kowalczyk, Adriaan P. IJzerman and Gerard J. P. van Westen

Efficiency of different measures for defining the applicability domain of classification models

The goal of defining an applicability domain for a predictive classification model is to identify the region in chemical space where the model’s predictions are reliable. The boundary of the applicability doma...

Authors: Waldemar Klingspohn, Miriam Mathea, Antonius ter Laak, Nikolaus Heinrich and Knut Baumann

Data driven polypharmacological drug design for lung cancer: analyses for targeting ALK, MET, and EGFR

Drug design of protein kinase inhibitors is now greatly enabled by thousands of publicly available X-ray structures, extensive ligand binding data, and optimized scaffolds coming off patent. The extensive dat...

Authors: Dilip Narayanan, Osman A. B. S. M. Gani, Franz X. E. Gruber and Richard A. Engh

Deep-learning: investigating deep neural networks hyper-parameters and comparison of performance to shallow methods for modeling bioactivity data

In recent years, research in artificial neural networks has resurged, now under the deep-learning umbrella, and grown extremely popular. Recently reported success of DL techniques in crowd-sourced QSAR and pre...

Authors: Alexios Koutsoukas, Keith J. Monaghan, Xiaoli Li and Jun Huan

Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D

The mechanism of each chemical reaction in a metabolic network can be represented as a set of atom mappings, each of which relates an atom in a substrate metabolite to an atom of the same element in a product ...

Authors: German A. Preciat Gonzalez, Lemmer R. P. El Assal, Alberto Noronha, Ines Thiele, Hulda S. Haraldsdóttir and Ronan M. T. Fleming

Helping to improve the practice of cheminformatics

Authors: Rajarshi Guha and Egon Willighagen

Erratum to: ExCAPE-DB: an integrated large scale dataset facilitating Big Data analysis in chemogenomics

Authors: Jiangming Sun, Nina Jeliazkova, Vladimir Chupakhin, Jose-Felipe Golib-Dzib, Ola Engkvist, Lars Carlsson, Jörg Wegner, Hugo Ceulemans, Ivan Georgiev, Vedrin Jeliazkov, Nikolay Kochev, Thomas J. Ashby and Hongming Chen