Designing drugs when there is low data availability: one-shot learning and other approaches to face the issues of a long-term concern

GC Verissimo, MSM Serafim… - Expert Opinion on …, 2022 - Taylor & Francis
Introduction Modern drug discovery is generally accessed by useful information from
previous large databases or uncovering novel data. The lack of biological and/or chemical …

Curse and Blessing of Non‐Proteinogenic Parts in Computational Enzyme Engineering

KT Korbeld, MJLJ Fürst - ChemBioChem, 2023 - Wiley Online Library
Enzyme engineering aims to improve or install a new function in biocatalysts for applications
ranging from chemical synthesis to biomedicine. For decades, computational techniques …

Deep generative model for therapeutic targets using transcriptomic disease-associated data—USP7 case study

T Pereira, M Abbasi, RI Oliveira… - Briefings in …, 2022 - academic.oup.com
The generation of candidate hit molecules with the potential to be used in cancer treatment
is a challenging task. In this context, computational methods based on deep learning have …

Identification of LASSBio-1945 as an inhibitor of SARS-CoV-2 main protease (M PRO) through in silico screening supported by molecular docking and a fragment …

LS Franco, RC Maia, EJ Barreiro - RSC medicinal chemistry, 2021 - pubs.rsc.org
In December 2019, an infectious disease was detected in Wuhan, China, caused by a new
pathogenic coronavirus, named SARS-CoV-2. It spread very rapidly, and on March 11th of …

Fragment localized molecular orbitals

T Giovannini, H Koch - Journal of Chemical Theory and …, 2022 - ACS Publications
We introduce the concept of fragment localized molecular orbitals (FLMOs), which are
Hartree–Fock molecular orbitals localized in specific fragments constituting a molecular …

Artificial intelligence for prediction of biological activities and generation of molecular hits using stereochemical information

TO Pereira, M Abbasi, RI Oliveira, RA Guedes… - Journal of Computer …, 2023 - Springer
In this work, we develop a method for generating targeted hit compounds by applying deep
reinforcement learning and attention mechanisms to predict binding affinity against a …

Discovery of Oral Anticancer 1,2-Bis(hydroxymethyl)benzo[g]pyrrolo[2,1-a]phthalazine Hybrids That Inhibit Angiogenesis and Induce DNA Cross-Links

TL Chen, AS Patel, V Jain, R Kuppusamy… - Journal of Medicinal …, 2021 - ACS Publications
Designing hybrid molecules with dual functions is one approach to improve the therapeutic
efficacy of combination treatment. We have previously conjugated phthalazine and bis …

FOCUS on NOD2: Advancing IBD Drug Discovery with a User-Informed Machine Learning Framework

R Choudhary, R Mahadevan - ACS Medicinal Chemistry Letters, 2024 - ACS Publications
In this study, we introduce the Framework for Optimized Customizable User-Informed
Synthesis (FOCUS), a generative machine learning model tailored for drug discovery …

[HTML][HTML] Kohn–Sham fragment energy decomposition analysis

T Giovannini - The Journal of Chemical Physics, 2024 - pubs.aip.org
We introduce the concept of Kohn–Sham fragment localized molecular orbitals (KS-FLMOs),
which are Kohn–Sham molecular orbitals (MOs) localized in specific fragments constituting …

Coumarins as Potential Antiprotozoal Agents: Biological Activities and Mechanism of Action

EJT Sierra, CF Cordeiro, L de Figueiredo Diniz… - Revista Brasileira de …, 2021 - Springer
Since the discovery of dicoumarol (a coumarin-based anticoagulant) in 1940, coumarins
have been found to possess a range of biological activities such as antimicrobial, anti …