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JCIM & JCTC Journals @JCIM_JCTC

Tweets from Journal of Chemical Information and Modeling (JCIM) and Journal of Chemical Theory and Computation (JCTC) from @ACSPublications

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JCIM & JCTC Journals@JCIM_JCTC
Jun 5
📢 Check the new Volume 66 Issue 9 of #JCIM pubs.acs.org/toc/jcisd8/66/9
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mDADGAN: Predicting miRNA–Drug Response Associations Using lncRNAs and a Diffusion-Based Generative Adversarial Network pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue9 #compchem

mDADGAN: Predicting miRNA–Drug Response Associations Using lncRNAs and a Diffusion-Based Generative...

MicroRNAs (miRNAs) are key regulators of anticancer drug response, including sensitivity and resistance. Accurate prediction of miRNA–drug response associations is important for understanding...

pubs.acs.org
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Hydrogen-Bonding Changes Cause Differences in Imipenem Breakdown Activity in OXA-48 Variants pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue9 #compchem

Hydrogen-Bonding Changes Cause Differences in Imipenem Breakdown Activity in OXA-48 Variants

The β-lactamase OXA-48 efficiently hydrolyzes carbapenem antibiotics, especially imipenem. Carbapenem resistance is a rising clinical concern and is frequently associated with OXA-48 and its varian...

pubs.acs.org
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Structural and Energetic Basis of Ca2 -Selective Permeation in the TRPV5 Channel pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue9 #compchem

Structural and Energetic Basis of Ca2 -Selective Permeation in the TRPV5 Channel

TRPV5 is a calcium-selective epithelial ion channel that is essential for renal Ca2 reabsorption and systemic calcium homeostasis. Despite recent structural advances, the energetic basis and...

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CapsBAM-ac4C: An Attention Mechanism-Enhanced Capsule Networks for RNA N4-Acetylcytidine Site Prediction pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue9 #compchem

CapsBAM-ac4C: An Attention Mechanism-Enhanced Capsule Networks for RNA N4-Acetylcytidine Site...

N4-acetylcytidine (ac4C) modification is crucial for gene expression regulation. However, existing prediction methods are limited by one-dimensional sequence encodings, which inadequately capture the...

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MechMemDyn: Coupling Frustration Analysis with Membrane Dynamics to Target the TREM2-DAP12 Complex Interface pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue9 #compchem

MechMemDyn: Coupling Frustration Analysis with Membrane Dynamics to Target the TREM2-DAP12 Complex...

The transmembrane complex formed by TREM2 (Triggering Receptor Expressed on Myeloid cells 2) and DAP12 (DNAX-activating protein of 12 kDa) constitutes a pivotal therapeutic target for Alzheimer’s...

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Free Energy and Flexibility Analysis of Autoinhibited Human BRAF pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue9 #compchem

Free Energy and Flexibility Analysis of Autoinhibited Human BRAF

The RAF serine/threonine protein kinases function as direct effectors of RAS in the intracellular transmission of extracellular growth signals, and they are key targets for drug discovery, given the...

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Molecular Behavior of Human β Defensin Type 3 Embedded in Different Model Lipid Membranes pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue9 #compchem

Molecular Behavior of Human β Defensin Type 3 Embedded in Different Model Lipid Membranes

Human β defensin type 3 (hBD-3) is recognized as one of the most intriguing antimicrobial peptides (AMPs) that holds the promise of solving drug resistance issues. hBD-3 can function (disruption of...

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Accurate Determination of Host–Guest Standard Binding Free Energies and Kinetic Parameters from Replica Exchange Molecular Dynamics Simulation pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue9 #compchem

Accurate Determination of Host–Guest Standard Binding Free Energies and Kinetic Parameters from...

Accurate prediction of drug kinetic rates is critical for rational drug design, especially since the drug residence time has been shown to correlate strongly with its efficacy. Molecular dynamics...

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Temperature-Induced Lipid Remodeling Underpins Thermal Resilience in Marine Macroalgae via Homeoviscous Membrane Adaptation: Bridging Experiments and Atomistic Simulations pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue9 #compchem

Temperature-Induced Lipid Remodeling Underpins Thermal Resilience in Marine Macroalgae via Homeov...

Marine macroalgae are vital primary producers of coastal ecosystems and natural sources of industrially-important bioactive compounds. Temperature governs their productivity, while ocean warming and...

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Comparative Assessment of Free Energy Computational Methods for Revealing the Interactions Driving PARP1 Selective Inhibition pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue9 #compchem

Comparative Assessment of Free Energy Computational Methods for Revealing the Interactions Driving...

Accurate prediction of inhibitor selectivity across protein paralogues remains a central challenge in computational drug discovery. Here, we perform a comparative assessment of three computational...

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Comprehensive Assessment and Benchmark of Deep Generative Models for Proteolysis TArgeting Chimera (PROTAC) Design pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue9 #compchem

Comprehensive Assessment and Benchmark of Deep Generative Models for Proteolysis TArgeting Chimera...

Proteolysis TArgeting Chimera (PROTAC) has been constantly proven to be an effective strategy for targeted protein degradation. More recently, various deep generative models have been proposed and...

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A Comprehensive Benchmark Database of Per- and Polyfluoroalkyl Substance Properties from Quantum Mechanical Methods pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue9 #compchem

A Comprehensive Benchmark Database of Per- and Polyfluoroalkyl Substance Properties from Quantum...

Per- and polyfluoroalkyl substances (PFAS) remain challenging for quantum mechanical (QM) modeling due to their atypical electronic structures, large number of compounds, and limited experimental...

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Martini Mapper: An Automated Fragment-Based Mapping Algorithm for Developing Coarse-Grained Models within the Martini 3 Framework pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue9 #compchem

Martini Mapper: An Automated Fragment-Based Mapping Algorithm for Developing Coarse-Grained Models...

Coarse-graining (CG) reduces molecular details to extend the time and length scales of molecular dynamics simulations to microseconds and micrometers. However, the CG approaches have long been...

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Defining a Chemical Space of π-Conjugated Hydrocarbons by Unit-Based Construction pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue9 #ChemicalInformation

Defining a Chemical Space of π-Conjugated Hydrocarbons by Unit-Based Construction

Ď€-Conjugated hydrocarbons are foundational molecular scaffolds in materials science. However, their design and discovery are limited by the lack of systematic frameworks for exploring their chemical...

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Mathematical State Function Structure Matters in Metal Oxide Reduction Thermodynamic Modeling pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue9 #ChemicalInformation

Mathematical State Function Structure Matters in Metal Oxide Reduction Thermodynamic Modeling

Thermodynamic modeling investigations commonly focus on data sufficiency, regularization strategies, and optimizer choice, implicitly assuming that mathematically equivalent state function formulat...

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Rational Design of Single-Phase High-Entropy Oxides via Large Language Model Data Mining and Explainable Machine Learning pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue9 #MachineLearning #DeepLearning

Rational Design of Single-Phase High-Entropy Oxides via Large Language Model Data Mining and...

The rational design of high-entropy oxides (HEOs) is currently hindered by the scarcity of structured property data in the scientific literature. In this work, we present an end-to-end materials...

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CGDock: Curvature-Aware Geometric Flow Framework for Protein-Ligand Docking pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue9 #MachineLearning #DeepLearning

CGDock: Curvature-Aware Geometric Flow Framework for Protein-Ligand Docking

Accurately predicting the conformation of small-molecule ligands to protein targets is a critical step in drug discovery and therapeutic development. Although deep learning has enabled substantial...

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Predicting Peptide Aggregation with Protein Language Model Embeddings pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue9 #MachineLearning #DeepLearning

Predicting Peptide Aggregation with Protein Language Model Embeddings

Amyloid fibrils, a form of peptide aggregates, are associated with multiple diseases and hinder the development of therapeutics. The experimental characterization of aggregating peptides is resourc...

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VeGA-RX and VeGA-SCX: Controllable SMARTS-Guided Generative Transformers for Precision-DrivenDe NovoDrug Design pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue9 #MachineLearning #DeepLearning

VeGA-RX and VeGA-SCX: Controllable SMARTS-Guided Generative Transformers for Precision-Driven De...

Generative models enable large-scale exploration of chemical space; however, achieving controllable generation that balances novelty with preservation of bioactive features remains challenging. In...

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Learning Electronic Polarization in Molecular Systems: Vibrational Spectroscopy of Ethanol–Water Mixtures pubs.acs.org/doi/10.1021/acs… #JCIM Vol66 Issue9 #MachineLearning #DeepLearning

Learning Electronic Polarization in Molecular Systems: Vibrational Spectroscopy of Ethanol–Water...

Mixtures of water and ethanol are an important solvent for biochemical reactions, as well as being a model system for hydrophobic hydration, since the ethanol molecule consists of polar and nonpolar...

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