AIMC Topic: Molecular Docking Simulation

Clear Filters Showing 771 to 780 of 854 articles

DRLiPS: a novel method for prediction of druggable RNA-small molecule binding pockets using machine learning.

Nucleic acids research
Ribonucleic Acid (RNA) is the central conduit for information transfer in the cell. Identifying potential RNA targets in disease conditions is a challenging task, given the vast repertoire of functional non-coding RNAs in a human cell. A potential dr...

Increase Docking Score Screening Power by Simple Fusion With CNNscore.

Journal of computational chemistry
Scoring functions (SFs) of molecular docking is a vital component of structure-based virtual screening (SBVS). Traditional SFs yield their inherent shortage for idealized approximations and simplifications predicting the binding affinity. Complementa...

TopoQA: a topological deep learning-based approach for protein complex structure interface quality assessment.

Briefings in bioinformatics
Even with the significant advances of AlphaFold-Multimer (AF-Multimer) and AlphaFold3 (AF3) in protein complex structure prediction, their accuracy is still not comparable with monomer structure prediction. Efficient and effective quality assessment ...

Machine Learning-Based Discovery of a Novel Noncovalent MurA Inhibitor as an Antibacterial Agent.

Chemical biology & drug design
The bacterial cell wall is crucial for maintaining the integrity of bacterial cells. UDP-N-acetylglucosamine 1-carboxyethylene transferase (MurA) is an important enzyme involved in bacterial cell wall synthesis. Therefore, it is an important target f...

Discovery of New HER2 Inhibitors via Computational Docking, Pharmacophore Modeling, and Machine Learning.

Molecular informatics
The human epidermal growth factor receptor 2 (HER2) is a critical oncogene implicated in the development of various aggressive cancers, particularly breast cancer. Discovering novel HER2 inhibitors is crucial for expanding therapeutic options for HER...

Integrative machine learning approach for identification of new molecular scaffold and prediction of inhibition responses in cancer cells using multi-omics data.

Briefings in functional genomics
MDM2 (Mouse Double Minute 2), a fundamental governor of the p53 tumor suppressor pathway, has garnered significant attention as a favorable target for cancer therapy. Recent years have witnessed the development and synthesis of potent MDM2 inhibitors...

Identifying Common Diagnostic Biomarkers and Therapeutic Targets between COPD and Sepsis: A Bioinformatics and Machine Learning Approach.

International journal of chronic obstructive pulmonary disease
BACKGROUND: Evidence suggests a bidirectional association between chronic obstructive pulmonary disease (COPD) and sepsis, but the underlying mechanisms remain unclear. This study aimed to explore shared diagnostic genes, potential mechanisms, and th...

Identification and validation of shared biomarkers and drug repurposing in psoriasis and Crohn's disease: integrating bioinformatics, machine learning, and experimental approaches.

Frontiers in immunology
BACKGROUND: Psoriasis and Crohn's disease (CD) are chronic inflammatory diseases that involve complex immune-mediated mechanisms. Despite clinical overlap and shared genetic predispositions, the molecular pathways connecting these diseases remain inc...

SG-ML-PLAP: A structure-guided machine learning-based scoring function for protein-ligand binding affinity prediction.

Protein science : a publication of the Protein Society
Computational methods to predict binding affinity of protein-ligand complex have been used extensively to design inhibitors for proteins selected as drug targets. In recent years machine learning (ML) is being increasingly used for design of drugs/in...