Application advances of deep learning methods for de novo drug design and molecular dynamics simulation

Q Bai, S Liu, Y Tian, T Xu… - Wiley …, 2022 - Wiley Online Library
De novo drug design is a stationary way to build novel ligands in the confined pocket of
receptor by assembling the atoms or fragments, while molecular dynamics (MD) simulation …

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 …

AutoGrow4: an open-source genetic algorithm for de novo drug design and lead optimization

JO Spiegel, JD Durrant - Journal of cheminformatics, 2020 - Springer
We here present AutoGrow4, an open-source program for semi-automated computer-aided
drug discovery. AutoGrow4 uses a genetic algorithm to evolve predicted ligands on demand …

FFLOM: A flow-based autoregressive model for fragment-to-lead optimization

J **, D Wang, G Shi, J Bao, J Wang… - Journal of Medicinal …, 2023 - ACS Publications
Recently, deep generative models have been regarded as promising tools in fragment-
based drug design (FBDD). Despite the growing interest in these models, they still face …

Virtual screening web servers: designing chemical probes and drug candidates in the cyberspace

N Singh, L Chaput, BO Villoutreix - Briefings in bioinformatics, 2021 - academic.oup.com
The interplay between life sciences and advancing technology drives a continuous cycle of
chemical data growth; these data are most often stored in open or partially open databases …

PepScaf: Harnessing Machine Learning with In Vitro Selection toward De Novo Macrocyclic Peptides against IL-17C/IL-17RE Interaction

S Zhai, Y Tan, C Zhang, CJ Hipolito… - Journal of Medicinal …, 2023 - ACS Publications
The combination of library-based screening and artificial intelligence (AI) has been
accelerating the discovery and optimization of hit ligands. However, the potential of AI to …

Deep Lead Optimization: Leveraging Generative AI for Structural Modification

O Zhang, H Lin, H Zhang, H Zhao… - Journal of the …, 2024 - ACS Publications
The integration of deep learning-based molecular generation models into drug discovery
has garnered significant attention for its potential to expedite the development process …

Fragment based drug design: from experimental to computational approaches

A Kumar, A Voet, KYJ Zhang - Current medicinal chemistry, 2012 - ingentaconnect.com
Fragment based drug design has emerged as an effective alternative to high throughput
screening for the identification of lead compounds in drug discovery in the past fifteen years …

ACFIS: a web server for fragment-based drug discovery

GF Hao, W Jiang, YN Ye, FX Wu, XL Zhu… - Nucleic acids …, 2016 - academic.oup.com
In order to foster innovation and improve the effectiveness of drug discovery, there is a
considerable interest in exploring unknown 'chemical space'to identify new bioactive …

De novo drug design

M Hartenfeller, G Schneider - Chemoinformatics and computational …, 2011 - Springer
Computer-assisted molecular design supports drug discovery by suggesting novel
chemotypes and compound modifications for lead structure optimization. While the aspect of …