AIMC Topic: Models, Molecular

Clear Filters Showing 81 to 90 of 657 articles

Deciphering Molecular Embeddings with Centered Kernel Alignment.

Journal of chemical information and modeling Sep 25, 2024
Analyzing machine learning models, especially nonlinear ones, poses significant challenges. In this context, centered kernel alignment (CKA) has emerged as a promising model analysis tool that assesses the similarity between two embeddings. CKA's eff...
Neural Networks, Computer Machine Learning Cheminformatics Algorithms Models, Molecular
View on PubMed DOI

In Silico Insights: QSAR Modeling of TBK1 Kinase Inhibitors for Enhanced Drug Discovery.

Journal of chemical information and modeling Sep 17, 2024
TBK1, or TANK-binding kinase 1, is an enzyme that functions as a serine/threonine protein kinase. It plays a crucial role in various cellular processes, including the innate immune response to viruses, cell proliferation, apoptosis, autophagy, and an...
Quantitative Structure-Activity Relationship Protein Kinase Inhibitors Machine Learning Computer Simulation Protein Serine-Threonine Kinases Models, Molecular Drug Discovery Humans
View on PubMed DOI

A Machine Learning Method for RNA-Small Molecule Binding Preference Prediction.

Journal of chemical information and modeling Sep 12, 2024
The interaction between RNA and small molecules is crucial in various biological functions. Identifying molecules targeting RNA is essential for the inhibitor design and RNA-related studies. However, traditional methods focus on learning RNA sequence...
RNA Nucleic Acid Conformation Small Molecule Libraries Machine Learning Models, Molecular
View on PubMed DOI

Toward the Integration of Machine Learning and Molecular Modeling for Designing Drug Delivery Nanocarriers.

Advanced materials (Deerfield Beach, Fla.) Sep 10, 2024
The pioneering work on liposomes in the 1960s and subsequent research in controlled drug release systems significantly advances the development of nanocarriers (NCs) for drug delivery. This field is evolved to include a diverse array of nanocarriers ...
Humans Drug Design Nanoparticles Drug Carriers Machine Learning Drug Delivery Systems Models, Molecular
View on PubMed DOI

Prediction of Inhibitory Activity against the MATE1 Transporter via Combined Fingerprint- and Physics-Based Machine Learning Models.

Journal of chemical information and modeling Sep 10, 2024
Renal secretion plays an important role in excretion of drug from the kidney. Two major transporters known to be highly involved in renal secretion are MATE1/2 K and OCT2, the former of which is highly related to drug-drug interactions. Among publish...
Organic Cation Transport Proteins Machine Learning Models, Molecular Humans Neural Networks, Computer
View on PubMed DOI

Modelling protein complexes with crosslinking mass spectrometry and deep learning.

Nature communications Sep 9, 2024
Scarcity of structural and evolutionary information on protein complexes poses a challenge to deep learning-based structure modelling. We integrate experimental distance restraints obtained by crosslinking mass spectrometry (MS) into AlphaFold-Multim...
Models, Molecular Bacillus subtilis Iron Deep Learning Mass Spectrometry Protein Conformation Cross-Linking Reagents Bacterial Proteins
View on PubMed DOI

Pretrainable geometric graph neural network for antibody affinity maturation.

Nature communications Sep 6, 2024
Increasing the binding affinity of an antibody to its target antigen is a crucial task in antibody therapeutics development. This paper presents a pretrainable geometric graph neural network, GearBind, and explores its potential in in silico affinity...
Computer Simulation Deep Learning Protein Binding Humans Neural Networks, Computer Antibodies Antigens Antibody Affinity Enzyme-Linked Immunosorbent Assay Models, Molecular
View on PubMed DOI

Conformational Space Profiling Enhances Generic Molecular Representation for AI-Powered Ligand-Based Drug Discovery.

Advanced science (Weinheim, Baden-Wurttemberg, Germany) Aug 29, 2024
The molecular representation model is a neural network that converts molecular representations (SMILES, Graph) into feature vectors, and is an essential module applied across a wide range of artificial intelligence-driven drug discovery scenarios. Ho...
Ligands Drug Discovery Molecular Conformation Models, Molecular Neural Networks, Computer Artificial Intelligence
View on PubMed DOI

Predicting the Binding of Small Molecules to Proteins through Invariant Representation of the Molecular Structure.

Journal of chemical information and modeling Aug 28, 2024
We present a computational scheme for predicting the ligands that bind to a pocket of a known structure. It is based on the generation of a general abstract representation of the molecules, which is invariant to rotations, translations, and permutati...
Molecular Structure Ligands Proteins Models, Molecular Small Molecule Libraries Protein Conformation Algorithms Machine Learning Binding Sites Protein Binding
View on PubMed DOI

An end-to-end framework for the prediction of protein structure and fitness from single sequence.

Nature communications Aug 27, 2024
Significant research progress has been made in the field of protein structure and fitness prediction. Particularly, single-sequence-based structure prediction methods like ESMFold and OmegaFold achieve a balance between inference speed and prediction...
Protein Stability Protein Conformation Sequence Analysis, Protein Models, Molecular Mutation Computational Biology Proteins Neural Networks, Computer Algorithms
View on PubMed DOI
Popular Topics
Recent Journals