In silico Strategies to Support Fragment-to-Lead Optimization in Drug Discovery

LR de Souza Neto, JT Moreira-Filho, BJ Neves… - Frontiers in …, 2020 - frontiersin.org
Fragment-based drug (or lead) discovery (FBDD or FBLD) has developed in the last two
decades to become a successful key technology in the pharmaceutical industry for early …

Generating focused molecule libraries for drug discovery with recurrent neural networks

MHS Segler, T Kogej, C Tyrchan… - ACS central science, 2018 - ACS Publications
In de novo drug design, computational strategies are used to generate novel molecules with
good affinity to the desired biological target. In this work, we show that recurrent neural …

Learning continuous and data-driven molecular descriptors by translating equivalent chemical representations

R Winter, F Montanari, F Noé, DA Clevert - Chemical science, 2019 - pubs.rsc.org
There has been a recent surge of interest in using machine learning across chemical space
in order to predict properties of molecules or design molecules and materials with the …

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

EL Willighagen, JW Mayfield, J Alvarsson… - Journal of …, 2017 - Springer
Abstract Background The Chemistry Development Kit (CDK) is a widely used open source
cheminformatics toolkit, providing data structures to represent chemical concepts along with …

Cheminformatics in drug discovery, an industrial perspective

H Chen, T Kogej, O Engkvist - Molecular Informatics, 2018 - Wiley Online Library
Cheminformatics has established itself as a core discipline within large scale drug discovery
operations. It would be impossible to handle the amount of data generated today in a small …

Predicting PC-SAFT pure-component parameters by machine learning using a molecular fingerprint as key input

J Habicht, C Brandenbusch, G Sadowski - Fluid Phase Equilibria, 2023 - Elsevier
In this work, a machine learning (ML)-approach was developed to predict pure-component
parameters for the Perturbed-Chain Statistical Associating Fluid Theory (PC-SAFT) for non …

Prototype-based compound discovery using deep generative models

S Harel, K Radinsky - Molecular pharmaceutics, 2018 - ACS Publications
Designing a new drug is a lengthy and expensive process. As the space of potential
molecules is very large (Polishchuk, PG; Madzhidov, TI; Varnek, A. Estimation of the size of …

Predicting novel substrates for enzymes with minimal experimental effort with active learning

DA Pertusi, ME Moura, JG Jeffryes, S Prabhu… - Metabolic …, 2017 - Elsevier
Enzymatic substrate promiscuity is more ubiquitous than previously thought, with significant
consequences for understanding metabolism and its application to biocatalysis. This …

MolTarPred: a web tool for comprehensive target prediction with reliability estimation

A Peón, H Li, G Ghislat, KS Leung… - Chemical biology & …, 2019 - Wiley Online Library
Molecular target prediction can provide a starting point to understand the efficacy and side
effects of phenotypic screening hits. Unfortunately, the vast majority of in silico target …

Predicting off-target binding profiles with confidence using conformal prediction

S Lampa, J Alvarsson, S Arvidsson Mc Shane… - Frontiers in …, 2018 - frontiersin.org
Ligand-based models can be used in drug discovery to obtain an early indication of
potential off-target interactions that could be linked to adverse effects. Another application is …