De Novo Molecule Design Using Molecular Generative Models Constrained by Ligand–Protein Interactions

J Zhang, H Chen - Journal of chemical information and modeling, 2022 - ACS Publications
In recent years, molecular deep generative models have attracted much attention for its
application in de novo drug design. The data-driven molecular deep generative model …

ProLIF: a library to encode molecular interactions as fingerprints

C Bouysset, S Fiorucci - Journal of cheminformatics, 2021 - Springer
Interaction fingerprints are vector representations that summarize the three-dimensional
nature of interactions in molecular complexes, typically formed between a protein and a …

Prioritizing virtual screening with interpretable interaction fingerprints

AV Fassio, L Shub, L Ponzoni, J McKinley… - Journal of Chemical …, 2022 - ACS Publications
Machine learning-based drug discovery success depends on molecular representation. Yet
traditional molecular fingerprints omit both the protein and pointers back to structural …

fingeRNAt—A novel tool for high-throughput analysis of nucleic acid-ligand interactions

NA Szulc, Z Mackiewicz, JM Bujnicki… - PLoS computational …, 2022 - journals.plos.org
Computational methods play a pivotal role in drug discovery and are widely applied in
virtual screening, structure optimization, and compound activity profiling. Over the last …

Antispasmodic Effect of Alstonia boonei De Wild. and Its Constituents: Ex Vivo and In Silico Approaches

OJ Akinmurele, MA Sonibare, AA Elujoba… - Molecules, 2023 - mdpi.com
Background: Alstonia boonei, belonging to the family Apocynaceae, is one of the best-
known medicinal plants in Africa and Asia. Stem back preparations are traditionally used as …

PyPLIF HIPPOS and receptor ensemble docking increase the prediction accuracy of the structure-based virtual screening protocol targeting acetylcholinesterase

EP Istyastono, FDO Riswanto, N Yuniarti, VD Prasasty… - Molecules, 2022 - mdpi.com
In this article, the upgrading process of the structure-based virtual screening (SBVS) protocol
targeting acetylcholinesterase (AChE) previously published in 2017 is presented. The …

Building a kokumi database and machine learning-based prediction: a systematic computational study on kokumi analysis

Y He, K Liu, X Yu, H Yang, W Han - Journal of Chemical …, 2024 - ACS Publications
Kokumi is a subtle sensation characterized by a sense of fullness, continuity, and thickness.
Traditional methods of taste discovery and analysis, including those of kokumi, have been …

Identification of Peregrin inhibitors-modulators by harnessing the computational prowess of molecular simulation and machine learning algorithms

H Deka, AD Pawar, MS Battula, GE Eldesoky… - Journal of Molecular …, 2024 - Elsevier
Peregrin is marked as a potential drug target due to its pivotal role in the epigenetic
maintenance of cellular metabolism. It is counted among those of the bromodomain …

PredCoffee: A binary classification approach specifically for coffee odor

Y He, R Huang, R Zhang, F He, L Han, W Han - Iscience, 2024 - cell.com
Compared to traditional methods, using machine learning to assess or predict the odor of
molecules can save costs in various aspects. Our research aims to collect molecules with …

Hypoglycemic Activity of Rice Resistant-Starch Metabolites: A Mechanistic Network Pharmacology and In Vitro Approach

J Ren, J Dai, Y Chen, Z Wang, R Sha, J Mao, Y Mao - Metabolites, 2024 - mdpi.com
Rice (Oryza sativa L.) is one of the primary sources of energy and nutrients needed by the
body, and rice resistant starch (RRS) has been found to have hypoglycemic effects …