Consolidated knowledge-guided computational pipeline for therapeutic intervention against bacterial biofilms-a review

R Debroy, S Ramaiah - Biofouling, 2023 - Taylor & Francis
Biofilm-associated bacterial infections attributed to multifactorial antimicrobial resistance
have caused worldwide challenges in formulating successful treatment strategies. In search …

[HTML][HTML] An algorithm framework for Drug-Induced liver Injury Prediction based on genetic algorithm and ensemble learning

B Yan, X Ye, J Wang, J Han, L Wu, S He, K Liu, X Bo - Molecules, 2022 - mdpi.com
In the process of drug discovery, drug-induced liver injury (DILI) is still an active research
field and is one of the most common and important issues in toxicity evaluation research. It …

[HTML][HTML] Integrating transformers and many-objective optimization for drug design

N Aksamit, J Hou, Y Li, B Ombuki-Berman - BMC bioinformatics, 2024 - Springer
Background Drug design is a challenging and important task that requires the generation of
novel and effective molecules that can bind to specific protein targets. Artificial intelligence …

[HTML][HTML] SPOTLIGHT: structure-based prediction and optimization tool for ligand generation on hard-to-drug targets–combining deep reinforcement learning with …

VSS Adury, A Mukherjee - Digital Discovery, 2024 - pubs.rsc.org
We present SPOTLIGHT, a proof-of-concept for a method capable of designing a diverse set
of novel drug molecules through a rules-based approach. The model constructs molecules …

[HTML][HTML] Molecule auto-correction to facilitate molecular design

A Kerstjens, H De Winter - Journal of Computer-Aided Molecular Design, 2024 - Springer
Ensuring that computationally designed molecules are chemically reasonable is at best
cumbersome. We present a molecule correction algorithm that morphs invalid molecular …

Drug Discovery by Automated Adaptation of Chemical Structure and Identity

LA Patel, P Chau, S Debesai, L Darwin… - Journal of Chemical …, 2022 - ACS Publications
Computer-aided drug design offers the potential to dramatically reduce the cost and effort
required for drug discovery. While screening-based methods are valuable in the early …

Structure-Based Drug Design via 3D Molecular Generative Pre-training and Sampling

Y Yang, S Ouyang, X Hu, M Dang, M Zheng… - arXiv preprint arXiv …, 2024 - arxiv.org
Structure-based drug design aims at generating high affinity ligands with prior knowledge of
3D target structures. Existing methods either use conditional generative model to learn the …

Computer-aided de novo design and optimization of novel potential inhibitors of HIV-1 Nef protein

S Majumder, G Deganutti, L Pipitò, D Chaudhuri… - … Biology and Chemistry, 2023 - Elsevier
Nef is a small accessory protein pivotal in the HIV-1 viral replication cycle. It is a
multifunctional protein and its interactions with kinases in host cells have been well …

Structure-based Drug Design Benchmark: Do 3D Methods Really Dominate?

K Zheng, Y Lu, Z Zhang, Z Wan, Y Ma, M Zitnik… - arXiv preprint arXiv …, 2024 - arxiv.org
Currently, the field of structure-based drug design is dominated by three main types of
algorithms: search-based algorithms, deep generative models, and reinforcement learning …

Combining multi-objective evolutionary algorithms with deep generative models towards focused molecular design

T Sousa, J Correia, V Pereira, M Rocha - … 2021, Held as Part of EvoStar …, 2021 - Springer
Recent advances in applying deep generative learning to molecular design have led to a
large number of novel approaches to the targeted generation of molecules towards specific …