A comprehensive review of how Artificial Intelligence and Machine Learning are redefining this landscape across three critical dimensions outlines the transition toward end‐to‐end, adaptive discovery systems that ensure computational hits are biologically potent, structurally optimized, and synthetically accessible.
Abstract
Virtual screening (VS) on small molecules aims to identify promising drug candidates against protein targets from expansive chemical libraries by balancing the core requirements of accurate scoring and efficient search against the inherent trade‐off between accuracy and speed. This survey provides a comprehensive review of how Artificial Intelligence and Machine Learning (AI/ML) are redefining this landscape across three critical dimensions. First, we examine the evolution of AI‐driven scoring functions, which utilize AI/ML models to capture complex structure–activity relationships from massive biochemical datasets, significantly enhancing structure‐ and ligand‐based evaluations beyond traditional heuristics. Second, we summarize the emergence of efficient search algorithms that iteratively prioritize informative compounds to reduce search efforts by orders of magnitude. Third, we review the paradigm shift toward generative molecular design, making VS transition from screening fixed libraries to the
de novo
generation of molecules optimized for specific structural contexts and multi‐objective properties. This review outlines the transition toward end‐to‐end, adaptive discovery systems that ensure computational hits are biologically potent, structurally optimized, and synthetically accessible.
It is shown that prospective structure selection, rather than structure generation, represents the primary bottleneck in ensemble-based VS, highlighting an urgent need for novel structural descriptors to identify high-performing conformations.
Jaeoh Shin, K. Joo, Jejoong Yoo· Journal of Chemical Informat...· 1 citation
AdaptiveFlow enables drug discovery at unprecedented scale and supports the development of AI-driven methods, and identifies nanomolar inhibitors of two disease-relevant targets, ferroptosis suppressor protein 1 and poly(ADP-ribose) polymerase 1.
Domiziana Cecchini, AkshatKumar Nigam, Ming Tang et al.· Nature Biotechnology· 1 citation
The expansion of chemical space, advanced virtual screening, deep learning, molecular dynamics simulations, Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) modelling, and challenges for drug discovery are discussed.
Lun-Na Li, Lianna D. Soriano, W. M. Kedir et al.· Molecular Biomedicine· 0 citations
A state-aware functional classifier (SAFC) is developed that integrates molecular dynamics derived receptor ensembles, ensemble docking and protein ligand interaction graphs that provides dynamics-aware functional activity rankings for generated molecules that were partly complementary to docking, drug-likeness and syn...
H. Kumar, Zheng-Xiao Yang, Yankai Yu et al.· bioRxiv· 0 citations
A scalable, machine-learning-integrated virtual screening framework designed to explore ultra-large chemical space spanning an input search space of approximately 884 million compounds from ZINC20 and 199,854 purchasable compounds from the SPECS database is reported.
R. Muthuraj, Manasa Pacharla, Nehal Arvind Kumar et al.· Journal of Computer-Aided Mo...· 0 citations
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