Articles

Prediction of activity and selectivity profiles of human Carbonic Anhydrase inhibitors using machine learning classification models

The development of selective inhibitors of the clinically relevant human Carbonic Anhydrase (hCA) isoforms IX and XII has become a major topic in drug research, due to their deregulation in several types of ca...

Authors: Annachiara Tinivella, Luca Pinzi and Giulio Rastelli

Structure‐based identification of dual ligands at the A_2AR and PDE10A with anti‐proliferative effects in lung cancer cell‐lines

Enhanced/prolonged cAMP signalling has been suggested as a suppressor of cancer proliferation. Interestingly, two key modulators that elevate cAMP, the A_2A receptor (A_2AR) and phosphodiesterase 10A (PDE10A), are ...

Authors: Leen Kalash, Ian Winfield, Dewi Safitri, Marcel Bermudez, Sabrina Carvalho, Robert Glen, Graham Ladds and Andreas Bender

What is the role of cheminformatics in a pandemic?

Authors: Rajarshi Guha, Egon Willighagen, Barbara Zdrazil and Nina Jeliazkova

Hybrid semantic recommender system for chemical compounds in large-scale datasets

The large, and increasing, number of chemical compounds poses challenges to the exploration of such datasets. In this work, we propose the usage of recommender systems to identify compounds of interest to scie...

Authors: Marcia Barros, Andre Moitinho and Francisco M. Couto

Using GANs with adaptive training data to search for new molecules

The process of drug discovery involves a search over the space of all possible chemical compounds. Generative Adversarial Networks (GANs) provide a valuable tool towards exploring chemical space and optimizing...

Authors: Andrew E. Blanchard, Christopher Stanley and Debsindhu Bhowmik

MAIP: a web service for predicting blood‐stage malaria inhibitors

Malaria is a disease affecting hundreds of millions of people across the world, mainly in developing countries and especially in sub-Saharan Africa. It is the cause of hundreds of thousands of deaths each year...

Authors: Nicolas Bosc, Eloy Felix, Ricardo Arcila, David Mendez, Martin R. Saunders, Darren V. S. Green, Jason Ochoada, Anang A. Shelat, Eric J. Martin, Preeti Iyer, Ola Engkvist, Andreas Verras, James Duffy, Jeremy Burrows, J. Mark F. Gardner and Andrew R. Leach

Could graph neural networks learn better molecular representation for drug discovery? A comparison study of descriptor-based and graph-based models

Graph neural networks (GNN) has been considered as an attractive modelling method for molecular property prediction, and numerous studies have shown that GNN could yield more promising results than traditional...

Authors: Dejun Jiang, Zhenxing Wu, Chang-Yu Hsieh, Guangyong Chen, Ben Liao, Zhe Wang, Chao Shen, Dongsheng Cao, Jian Wu and Tingjun Hou

Incorporating structural similarity into a scoring function to enhance the prediction of binding affinities

In this study, we developed a novel algorithm to improve the screening performance of an arbitrary docking scoring function by recalibrating the docking score of a query compound based on its structure similar...

Authors: Beihong Ji, Xibing He, Yuzhao Zhang, Jingchen Zhai, Viet Hoang Man, Shuhan Liu and Junmei Wang

RegioSQM20: improved prediction of the regioselectivity of electrophilic aromatic substitutions

We present RegioSQM20, a new version of RegioSQM (Chem Sci 9:660, 2018), which predicts the regioselectivities of electrophilic aromatic substitution (EAS) reactions from the calculation of proton affinities. ...

Authors: Nicolai Ree, Andreas H. Göller and Jan H. Jensen

The kernel-weighted local polynomial regression (KwLPR) approach: an efficient, novel tool for development of QSAR/QSAAR toxicity extrapolation models

The ability of accurate predictions of biological response (biological activity/property/toxicity) of a given chemical makes the quantitative structure‐activity/property/toxicity relationship (QSAR/QSPR/QSTR) ...

Authors: Agnieszka Gajewicz-Skretna, Supratik Kar, Magdalena Piotrowska and Jerzy Leszczynski

ChemSpectra: a web-based spectra editor for analytical data

ChemSpectra, a web-based software to visualize and analyze spectroscopic data, integrating solutions for infrared spectroscopy (IR), mass spectrometry (MS), and one-dimensional ¹H and ¹³C NMR (proton and carbon n...

Authors: Yu-Chieh Huang, Pierre Tremouilhac, An Nguyen, Nicole Jung and Stefan Bräse

Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map

Protein solubility is significant in producing new soluble proteins that can reduce the cost of biocatalysts or therapeutic agents. Therefore, a computational model is highly desired to accurately predict prot...

Authors: Jianwen Chen, Shuangjia Zheng, Huiying Zhao and Yuedong Yang

ASFP (Artificial Intelligence based Scoring Function Platform): a web server for the development of customized scoring functions

Virtual screening (VS) based on molecular docking has emerged as one of the mainstream technologies of drug discovery due to its low cost and high efficiency. However, the scoring functions (SFs) implemented i...

Authors: Xujun Zhang, Chao Shen, Xueying Guo, Zhe Wang, Gaoqi Weng, Qing Ye, Gaoang Wang, Qiaojun He, Bo Yang, Dongsheng Cao and Tingjun Hou

Molecule Set Comparator (MSC): a CDK-based open rich‐client tool for molecule set similarity evaluations

The open rich-client Molecule Set Comparator (MSC) application enables a versatile and fast comparison of large molecule sets with a unique inter-set molecule-to-molecule mapping obtained e.g. by molecular-rec...

Authors: Kohulan Rajan, Jan-Mathis Hein, Christoph Steinbeck and Achim Zielesny

Substructure-based neural machine translation for retrosynthetic prediction

With the rapid improvement of machine translation approaches, neural machine translation has started to play an important role in retrosynthesis planning, which finds reasonable synthetic pathways for a target...

Authors: Umit V. Ucak, Taek Kang, Junsu Ko and Juyong Lee

Profiling and analysis of chemical compounds using pointwise mutual information

Pointwise mutual information (PMI) is a measure of association used in information theory. In this paper, PMI is used to characterize several publicly available databases (DrugBank, ChEMBL, PubChem and ZINC) i...

Authors: I. Čmelo, M. Voršilák and D. Svozil

COCONUT online: Collection of Open Natural Products database

Natural products (NPs) are small molecules produced by living organisms with potential applications in pharmacology and other industries as many of them are bioactive. This potential raised great interest in N...

Authors: Maria Sorokina, Peter Merseburger, Kohulan Rajan, Mehmet Aziz Yirik and Christoph Steinbeck

patRoon: open source software platform for environmental mass spectrometry based non-target screening

Mass spectrometry based non-target analysis is increasingly adopted in environmental sciences to screen and identify numerous chemicals simultaneously in highly complex samples. However, current data processin...

Authors: Rick Helmus, Thomas L. ter Laak, Annemarie P. van Wezel, Pim de Voogt and Emma L. Schymanski

From Big Data to Artificial Intelligence: chemoinformatics meets new challenges

The increasing volume of biomedical data in chemistry and life sciences requires development of new methods and approaches for their analysis. Artificial Intelligence and machine learning, especially neural ne...

Authors: Igor V. Tetko and Ola Engkvist

MET: a Java package for fast molecule equivalence testing

An important task in cheminformatics is to test whether two molecules are equivalent with respect to their 2D structure. Mathematically, this amounts to solving the graph isomorphism problem for labelled graph...

Authors: Jördis-Ann Schüler, Steffen Rechner and Matthias Müller-Hannemann

ReactionCode: format for reaction searching, analysis, classification, transform, and encoding/decoding

In the past two decades a lot of different formats for molecules and reactions have been created. These formats were mostly developed for the purposes of identifiers, representation, classification, analysis a...

Authors: Victorien Delannée and Marc C. Nicklaus

A ligand-based computational drug repurposing pipeline using KNIME and Programmatic Data Access: case studies for rare diseases and COVID-19

Biomedical information mining is increasingly recognized as a promising technique to accelerate drug discovery and development. Especially, integrative approaches which mine data from several (open) data sourc...

Authors: Alzbeta Tuerkova and Barbara Zdrazil

AiZynthFinder: a fast, robust and flexible open-source software for retrosynthetic planning

We present the open-source AiZynthFinder software that can be readily used in retrosynthetic planning. The algorithm is based on a Monte Carlo tree search that recursively breaks down a molecule to purchasable...

Authors: Samuel Genheden, Amol Thakkar, Veronika Chadimová, Jean-Louis Reymond, Ola Engkvist and Esben Bjerrum

LigGrep: a tool for filtering docked poses to improve virtual-screening hit rates

Structure-based virtual screening (VS) uses computer docking to prioritize candidate small-molecule ligands for subsequent experimental testing. Docking programs evaluate molecular binding in part by predictin...

Authors: Emily J. Ha, Cara T. Lwin and Jacob D. Durrant

Memory-assisted reinforcement learning for diverse molecular de novo design

In de novo molecular design, recurrent neural networks (RNN) have been shown to be effective methods for sampling and generating novel chemical structures. Using a technique called reinforcement learning (RL),...

Authors: Thomas Blaschke, Ola Engkvist, Jürgen Bajorath and Hongming Chen

Too sweet: cheminformatics for deglycosylation in natural products

Sugar units in natural products are pharmacokinetically important but often redundant and therefore obstructing the study of the structure and function of the aglycon. Therefore, it is recommended to remove th...

Authors: Jonas Schaub, Achim Zielesny, Christoph Steinbeck and Maria Sorokina

Structure–activity relationship-based chemical classification of highly imbalanced Tox21 datasets

The specificity of toxicant-target biomolecule interactions lends to the very imbalanced nature of many toxicity datasets, causing poor performance in Structure–Activity Relationship (SAR)-based chemical class...

Authors: Gabriel Idakwo, Sundar Thangapandian, Joseph Luttrell, Yan Li, Nan Wang, Zhaoxian Zhou, Huixiao Hong, Bei Yang, Chaoyang Zhang and Ping Gong

DECIMER: towards deep learning for chemical image recognition

The automatic recognition of chemical structure diagrams from the literature is an indispensable component of workflows to re-discover information about chemicals and to make it available in open-access databa...

Authors: Kohulan Rajan, Achim Zielesny and Christoph Steinbeck

Chemoinformatics-based enumeration of chemical libraries: a tutorial

Virtual compound libraries are increasingly being used in computer-assisted drug discovery applications and have led to numerous successful cases. This paper aims to examine the fundamental concepts of library...

Authors: Fernanda I. Saldívar-González, C. Sebastian Huerta-García and José L. Medina-Franco

Predicting in silico electron ionization mass spectra using quantum chemistry

Compound identification by mass spectrometry needs reference mass spectra. While there are over 102 million compounds in PubChem, less than 300,000 curated electron ionization (EI) mass spectra are available f...

Authors: Shunyang Wang, Tobias Kind, Dean J. Tantillo and Oliver Fiehn

Predicting target profiles with confidence as a service using docking scores

Identifying and assessing ligand-target binding is a core component in early drug discovery as one or more unwanted interactions may be associated with safety issues.

Authors: Laeeq Ahmed, Hiba Alogheli, Staffan Arvidsson McShane, Jonathan Alvarsson, Arvid Berg, Anders Larsson, Wesley Schaal, Erwin Laure and Ola Spjuth

Maximum common property: a new approach for molecular similarity

The maximum common property similarity (MCPhd) method is presented using descriptors as a new approach to determine the similarity between two chemical compounds or molecular graphs. This method uses the conce...

Authors: Aurelio Antelo-Collado, Ramón Carrasco-Velar, Nicolás García-Pedrajas and Gonzalo Cerruela-García

A review of optical chemical structure recognition tools

Structural information about chemical compounds is typically conveyed as 2D images of molecular structures in scientific documents. Unfortunately, these depictions are not a machine-readable representation of ...

Authors: Kohulan Rajan, Henning Otto Brinkhaus, Achim Zielesny and Christoph Steinbeck

Correction to: The chemfp project

An amendment to this paper has been published and can be accessed via the original article.

Authors: Andrew Dalke

Compressed graph representation for scalable molecular graph generation

Recently, deep learning has been successfully applied to molecular graph generation. Nevertheless, mitigating the computational complexity, which increases with the number of nodes in a graph, has been a major...

Authors: Youngchun Kwon, Dongseon Lee, Youn-Suk Choi, Kyoham Shin and Seokho Kang

Linking chemical and disease entities to ontologies by integrating PageRank with extracted relations from literature

Named Entity Linking systems are a powerful aid to the manual curation of digital libraries, which is getting increasingly costly and inefficient due to the information overload. Models based on the Personaliz...

Authors: Pedro Ruas, Andre Lamurias and Francisco M. Couto

Molecular representations in AI-driven drug discovery: a review and practical guide

The technological advances of the past century, marked by the computer revolution and the advent of high-throughput screening technologies in drug discovery, opened the path to the computational analysis and v...

Authors: Laurianne David, Amol Thakkar, Rocío Mercado and Ola Engkvist

EvoMol: a flexible and interpretable evolutionary algorithm for unbiased de novo molecular generation

The objective of this work is to design a molecular generator capable of exploring known as well as unfamiliar areas of the chemical space. Our method must be flexible to adapt to very different problems. Ther...

Authors: Jules Leguy, Thomas Cauchy, Marta Glavatskikh, Béatrice Duval and Benoit Da Mota

Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial

This paper is a tutorial developed for the data analysis platform Galaxy. The purpose of Galaxy is to make high-throughput computational data analysis, such as molecular dynamics, a structured, reproducible an...

Authors: Simon A. Bray, Tharindu Senapathi, Christopher B. Barnett and Björn A. Grüning

DeepGraphMolGen, a multi-objective, computational strategy for generating molecules with desirable properties: a graph convolution and reinforcement learning approach

We address the problem of generating novel molecules with desired interaction properties as a multi-objective optimization problem. Interaction binding models are learned from binding data using graph convolut...

Authors: Yash Khemchandani, Stephen O’Hagan, Soumitra Samanta, Neil Swainston, Timothy J. Roberts, Danushka Bollegala and Douglas B. Kell

CompRet: a comprehensive recommendation framework for chemical synthesis planning with algorithmic enumeration

In computer-assisted synthesis planning (CASP) programs, providing as many chemical synthetic routes as possible is essential for considering optimal and alternative routes in a chemical reaction network. As t...

Authors: Ryosuke Shibukawa, Shoichi Ishida, Kazuki Yoshizoe, Kunihiro Wasa, Kiyosei Takasu, Yasushi Okuno, Kei Terayama and Koji Tsuda

An open source chemical structure curation pipeline using RDKit

The ChEMBL database is one of a number of public databases that contain bioactivity data on small molecule compounds curated from diverse sources. Incoming compounds are typically not standardised according to...

Authors: A. Patrícia Bento, Anne Hersey, Eloy Félix, Greg Landrum, Anna Gaulton, Francis Atkinson, Louisa J. Bellis, Marleen De Veij and Andrew R. Leach

Neural machine translation of chemical nomenclature between English and Chinese

Machine translation of chemical nomenclature has considerable application prospect in chemical text data processing between languages. However, rule based machine translation tools have to face significant com...

Authors: Tingjun Xu, Weiming Chen, Junhong Zhou, Jingfang Dai, Yingyong Li and Yingli Zhao

spyrmsd: symmetry-corrected RMSD calculations in Python

Root mean square displacement (RMSD) calculations play a fundamental role in the comparison of different conformers of the same ligand. This is particularly important in the evaluation of protein-ligand dockin...

Authors: Rocco Meli and Philip C. Biggin

Atomic ring invariant and Modified CANON extended connectivity algorithm for symmetry perception in molecular graphs and rigorous canonicalization of SMILES

We propose new invariant (the product of the corresponding primes for the ring size of each bond of an atom) as a simple unambiguous ring invariant of an atom that allows distinguishing symmetry classes in the...

Authors: Dmytro G. Krotko

Adoption of the Citation Typing Ontology by the Journal of Cheminformatics

Authors: Egon Willighagen

A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions

Drug repositioning is the process of identifying novel therapeutic potentials for existing drugs and discovering therapies for untreated diseases. Drug repositioning, therefore, plays an important role in opti...

Authors: Tamer N. Jarada, Jon G. Rokne and Reda Alhajj

rMSIcleanup: an open-source tool for matrix-related peak annotation in mass spectrometry imaging and its application to silver-assisted laser desorption/ionization

Mass spectrometry imaging (MSI) has become a mature, widespread analytical technique to perform non-targeted spatial metabolomics. However, the compounds used to promote desorption and ionization of the analyt...

Authors: Gerard Baquer, Lluc Sementé, María García-Altares, Young Jin Lee, Pierre Chaurand, Xavier Correig and Pere Ràfols

DTiGEMS+: drug–target interaction prediction using graph embedding, graph mining, and similarity-based techniques

In silico prediction of drug–target interactions is a critical phase in the sustainable drug development process, especially when the research focus is to capitalize on the repositioning of existing drugs. How...

Authors: Maha A. Thafar, Rawan S. Olayan, Haitham Ashoor, Somayah Albaradei, Vladimir B. Bajic, Xin Gao, Takashi Gojobori and Magbubah Essack

One molecular fingerprint to rule them all: drugs, biomolecules, and the metabolome

Molecular fingerprints are essential cheminformatics tools for virtual screening and mapping chemical space. Among the different types of fingerprints, substructure fingerprints perform best for small molecule...

Authors: Alice Capecchi, Daniel Probst and Jean-Louis Reymond