AIMC Topic: Molecular Docking Simulation

Clear Filters Showing 821 to 830 of 854 articles

Cytotoxicity and molecular docking analysis of racemolactone I, a new sesquiterpene lactone isolated from .

Pharmaceutical biology
CONTEXT: Traditionally, Hook. f. (Asteraceae) has been reported to be effective in cancer treatment which motivated the authors to explore the plant for novel anticancer compounds.

The Impact of Crystallographic Data for the Development of Machine Learning Models to Predict Protein-Ligand Binding Affinity.

Current medicinal chemistry
BACKGROUND: One of the main challenges in the early stages of drug discovery is the computational assessment of protein-ligand binding affinity. Machine learning techniques can contribute to predicting this type of interaction. We may apply these tec...

Machine learning on ligand-residue interaction profiles to significantly improve binding affinity prediction.

Briefings in bioinformatics
Structure-based virtual screenings (SBVSs) play an important role in drug discovery projects. However, it is still a challenge to accurately predict the binding affinity of an arbitrary molecule binds to a drug target and prioritize top ligands from ...

Accurate prediction of inter-protein residue-residue contacts for homo-oligomeric protein complexes.

Briefings in bioinformatics
Protein-protein interactions play a fundamental role in all cellular processes. Therefore, determining the structure of protein-protein complexes is crucial to understand their molecular mechanisms and develop drugs targeting the protein-protein inte...

Accuracy or novelty: what can we gain from target-specific machine-learning-based scoring functions in virtual screening?

Briefings in bioinformatics
Machine-learning (ML)-based scoring functions (MLSFs) have gradually emerged as a promising alternative for protein-ligand binding affinity prediction and structure-based virtual screening. However, clouds of doubts have still been raised against the...

A modified binary particle swarm optimization with a machine learning algorithm and molecular docking for QSAR modelling of cholinesterase inhibitors.

SAR and QSAR in environmental research
The acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) inhibitors play a key role in treating Alzheimer's disease. This study proposes an approach that integrates a modified binary particle swarm optimization (PSO) with a machine learning ...

Computationally predicting binding affinity in protein-ligand complexes: free energy-based simulations and machine learning-based scoring functions.

Briefings in bioinformatics
Accurately predicting protein-ligand binding affinities can substantially facilitate the drug discovery process, but it remains as a difficult problem. To tackle the challenge, many computational methods have been proposed. Among these methods, free ...

The impact of compound library size on the performance of scoring functions for structure-based virtual screening.

Briefings in bioinformatics
Larger training datasets have been shown to improve the accuracy of machine learning (ML)-based scoring functions (SFs) for structure-based virtual screening (SBVS). In addition, massive test sets for SBVS, known as ultra-large compound libraries, ha...

Improving structure-based virtual screening performance via learning from scoring function components.

Briefings in bioinformatics
Scoring functions (SFs) based on complex machine learning (ML) algorithms have gradually emerged as a promising alternative to overcome the weaknesses of classical SFs. However, extensive efforts have been devoted to the development of SFs based on n...

Beware of the generic machine learning-based scoring functions in structure-based virtual screening.

Briefings in bioinformatics
Machine learning-based scoring functions (MLSFs) have attracted extensive attention recently and are expected to be potential rescoring tools for structure-based virtual screening (SBVS). However, a major concern nowadays is whether MLSFs trained for...