Natural product drug discovery in the artificial intelligence era

FI Saldívar-González, VD Aldas-Bulos… - Chemical …, 2022 - pubs.rsc.org
Natural products (NPs) are primarily recognized as privileged structures to interact with
protein drug targets. Their unique characteristics and structural diversity continue to marvel …

Chalcone derivatives: promising starting points for drug design

MN Gomes, EN Muratov, M Pereira, JC Peixoto… - Molecules, 2017 - mdpi.com
Medicinal chemists continue to be fascinated by chalcone derivatives because of their
simple chemistry, ease of hydrogen atom manipulation, straightforward synthesis, and a …

A systematic study of key elements underlying molecular property prediction

J Deng, Z Yang, H Wang, I Ojima, D Samaras… - Nature …, 2023 - nature.com
Artificial intelligence (AI) has been widely applied in drug discovery with a major task as
molecular property prediction. Despite booming techniques in molecular representation …

Computer-aided drug design methods

W Yu, AD MacKerell - Antibiotics: methods and protocols, 2017 - Springer
Computational approaches are useful tools to interpret and guide experiments to expedite
the antibiotic drug design process. Structure-based drug design (SBDD) and ligand-based …

Why is Tanimoto index an appropriate choice for fingerprint-based similarity calculations?

D Bajusz, A Rácz, K Héberger - Journal of cheminformatics, 2015 - Springer
Background Cheminformaticians are equipped with a very rich toolbox when carrying out
molecular similarity calculations. A large number of molecular representations exist, and …

Jaccard/Tanimoto similarity test and estimation methods for biological presence-absence data

NC Chung, BŻ Miasojedow, M Startek, A Gambin - BMC bioinformatics, 2019 - Springer
Background A survey of presences and absences of specific species across multiple
biogeographic units (or bioregions) are used in a broad area of biological studies from …

Comparative analysis of molecular fingerprints in prediction of drug combination effects

B Zagidullin, Z Wang, Y Guan… - Briefings in …, 2021 - academic.oup.com
Application of machine and deep learning methods in drug discovery and cancer research
has gained a considerable amount of attention in the past years. As the field grows, it …

Open-source platform to benchmark fingerprints for ligand-based virtual screening

S Riniker, GA Landrum - Journal of cheminformatics, 2013 - Springer
Similarity-search methods using molecular fingerprints are an important tool for ligand-
based virtual screening. A huge variety of fingerprints exist and their performance, usually …

MassGenie: A transformer-based deep learning method for identifying small molecules from their mass spectra

AD Shrivastava, N Swainston, S Samanta, I Roberts… - Biomolecules, 2021 - mdpi.com
The 'inverse problem'of mass spectrometric molecular identification ('given a mass spectrum,
calculate/predict the 2D structure of the molecule whence it came') is largely unsolved, and …

A comparison of 71 binary similarity coefficients: The effect of base rates

M Brusco, JD Cradit, D Steinley - Plos one, 2021 - journals.plos.org
There are many psychological applications that require collapsing the information in a two-
mode (eg, respondents-by-attributes) binary matrix into a one-mode (eg, attributes-by …