AIMC Topic: Molecular Dynamics Simulation

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Discovery of Tetrahydroisoquinoline-Based SARS-CoV-2 Helicase Inhibitors with Iterative, Deep Learning-Enhanced Virtual Screening.

Journal of chemical information and modeling
In this study, we pursued a structure-based drug discovery campaign targeting the SARS-CoV-2 helicase through three rounds of virtual screening (VS) enhanced with Artificial Intelligence (AI). The third round incorporated a deep neural network (DNN) ...

Solvent-Inclusive ML/MM Simulations: Assessments of Structural, Dynamical, and Thermodynamic Accuracy.

Journal of chemical information and modeling
Chemical reactions in solution are central to biological function, synthetic chemistry, and materials design. Accurate modeling of these systems is essential for obtaining mechanistic insights but remains computationally demanding. Hybrid machine-lea...

A Hybrid OPES-eABF Framework for Efficient Exploration and Data-Driven Collective Variable Discovery in Complex Free-Energy Landscapes.

Journal of chemical information and modeling
Molecular dynamics (MD) simulations are powerful tools for studying biomolecular systems, but they are fundamentally limited by accessible time scales, making the study of rare events such as protein folding or ligand unbinding computationally challe...

Machine learning-guided identification and simulation-based validation of potent JAK3 inhibitors for cancer therapy.

PloS one
Janus kinase 3 (JAK3) is a hematopoietic-specific kinase implicated in cytokine signaling and immune dysregulation and has recently been associated with cancer progression. However, selective and potent JAK3 inhibitors remain underdeveloped. In this ...

A Standardized Benchmark for Machine-Learned Molecular Dynamics Using Weighted Ensemble Sampling.

The journal of physical chemistry. B
The rapid evolution of molecular dynamics (MD) methods, including machine-learned dynamics, has outpaced the development of standardized tools for method validation. Objective comparison between simulation approaches is often hindered by inconsistent...

Computational screening and in vitro evaluation of sphingosine-1-phosphate analogues as therapeutics for Non-Hodgkin's lymphoma.

Scientific reports
Non-Hodgkin's lymphoma (NHL) is a prevalent hematological malignancy that includes a variety of B-cell and T-cell proliferations. The S1P (sphingosine-1-phosphate) pathway, involved in cell survival, proliferation, and migration, plays a critical rol...

Mechanistic Disruption of the TREM2-DAP12 Transmembrane Complex by Alzheimer's Disease Mutations: A Multiscale Simulation Study.

Journal of chemical information and modeling
Triggering receptor expressed on myeloid cell 2 (TREM2) is an immunomodulatory receptor that plays a critical role in microglial activation through its association with the adaptor protein DNAX-activation protein 12 (DAP12). Variants in TREM2 have be...

From Bits to Bonds: High-Throughput Virtual Screening of Ribonucleic Acid Nanocarriers Using a Combinatorial Approach of Machine Learning and Molecular Dynamics.

Journal of the American Chemical Society
The implementation of high-throughput methods for fuelling the design of effective nanocarriers for RNA delivery remains challenging. Traditional experimental screening is resource-intensive, while purely computational approaches face limitations, su...

Covalent: Interpretable and Discriminative Collective Variables Reveal Ligand-Dependent Switching in Human Cellular Retinol-Binding Protein 2.

Journal of chemical theory and computation
Identifying collective variables (CVs) that are both discriminative and interpretable remains a central challenge for enhanced sampling and mechanistic analysis of biomolecular systems. We present (), a supervised machine learning-based CV discovery...

Artificial intelligence in protein-based detection and inhibition of AMR pathways.

Journal of computer-aided molecular design
Antimicrobial Resistance (AMR) is a global concern demanding high-throughput and precise AMR surveillance strategies. This review provides a comprehensive list of Artificial Intelligence (AI) driven frameworks widely employed in the early detection, ...