AIMC Topic: Molecular Structure
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Synthetically Feasible De Novo Molecular Design of Leads Based on a Reinforcement Learning Model: AI-Assisted Discovery of an Anti-IBD Lead Targeting CXCR4.
Journal of medicinal chemistry
Jun 12, 2024
Artificial intelligence (AI) de novo molecular generation provides leads with novel structures for drug discovery. However, the target affinity and synthesizability of the generated molecules present critical challenges for the successful application...
Comparative Analysis of Chemical Descriptors by Machine Learning Reveals Atomistic Insights into Solute-Lipid Interactions.
Molecular pharmaceutics
May 23, 2024
This study explores the research area of drug solubility in lipid excipients, an area persistently complex despite recent advancements in understanding and predicting solubility based on molecular structure. To this end, this research investigated no...
Geometric deep learning methods and applications in 3D structure-based drug design.
Drug discovery today
May 16, 2024
3D structure-based drug design (SBDD) is considered a challenging and rational way for innovative drug discovery. Geometric deep learning is a promising approach that solves the accurate model training of 3D SBDD through building neural network model...
Protocol for creating representations of molecular structures using a polymer-specific decoder.
STAR protocols
May 2, 2024
To supply chemical structures of polymers for machine learning applications, decoding is necessary. Here, we present a protocol for generating polymer fingerprints (PFPs), which are representations of molecular structures, using a polymer-specific de...
Reactivities of acrylamide warheads toward cysteine targets: a QM/ML approach to covalent inhibitor design.
Journal of computer-aided molecular design
May 1, 2024
Covalent inhibition offers many advantages over non-covalent inhibition, but covalent warhead reactivity must be carefully balanced to maintain potency while avoiding unwanted side effects. While warhead reactivities are commonly measured with assays...
Artificial Intelligence-Assisted Optimization of Antipigmentation Tyrosinase Inhibitors: Molecular Generation Based on a Low Activity Lead Compound.
Journal of medicinal chemistry
Apr 23, 2024
Artificial intelligence (AI) molecular generation is a highly promising strategy in the drug discovery, with deep reinforcement learning (RL) models emerging as powerful tools. This study introduces a fragment-by-fragment growth RL forward molecular...
Building Uniformly Structured Polymer Memristors via a 2D Conjugation Strategy for Neuromorphic Computing.
Macromolecular rapid communications
Apr 21, 2024
Polymer memristors represent a highly promising avenue for the advancement of next-generation computing systems. However, the intrinsic structural heterogeneity characteristic of most polymers often results in organic polymer memristors displaying er...
GraphMHC: Neoantigen prediction model applying the graph neural network to molecular structure.
PloS one
Mar 27, 2024
Neoantigens are tumor-derived peptides and are biomarkers that can predict prognosis related to immune checkpoint inhibition by estimating their binding to major histocompatibility complex (MHC) proteins. Although deep neural networks have been prima...
Explainable artificial intelligence in the design of selective carbonic anhydrase I-II inhibitors via molecular fingerprinting.
Journal of computational chemistry
Mar 15, 2024
Inhibiting the enzymes carbonic anhydrase I (CA I) and carbonic anhydrase II (CA II) presents a potential avenue for addressing nervous system ailments such as glaucoma and Alzheimer's disease. Our study explored harnessing explainable artificial int...
Machine learning assisted methods for the identification of low toxicity inhibitors of Enoyl-Acyl Carrier Protein Reductase (InhA).
Computational biology and chemistry
Feb 20, 2024
Tuberculosis (TB) is one of the life-threatening infectious diseases with prehistoric origins and occurs in almost all habitable parts of the world. TB mainly affects the lungs, and its etiological agent is Mycobacterium tuberculosis (Mtb). In 2022, ...
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