AIMC Topic: Ligands

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Toward High-Throughput Predictive Modeling of Protein Binding/Unbinding Kinetics.

Journal of chemical information and modeling May 20, 2016
One of the unaddressed challenges in drug discovery is that drug potency determined in vitro is not a reliable indicator of drug activity in vivo. Accumulated evidence suggests that in vivo activity is more strongly correlated with the binding/unbind...
Machine Learning Drug Discovery Protein Binding Ligands Protein Conformation Static Electricity Thermodynamics Computational Biology Kinetics Molecular Dynamics Simulation Safety
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Machine learning optimization of cross docking accuracy.

Computational biology and chemistry May 4, 2016
Performance of small molecule automated docking programs has conceptually been divided into docking -, scoring -, ranking - and screening power, which focuses on the crystal pose prediction, affinity prediction, ligand ranking and database screening ...
Ligands Machine Learning Molecular Docking Simulation Drug Design
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Deciphering the Complexity of Ligand-Protein Recognition Pathways Using Supervised Molecular Dynamics (SuMD) Simulations.

Journal of chemical information and modeling Apr 14, 2016
Molecular recognition is a crucial issue when aiming to interpret the mechanism of known active substances as well as to develop novel active candidates. Unfortunately, simulating the binding process is still a challenging task because it requires cl...
Protein Conformation Protein Binding Receptors, G-Protein-Coupled Molecular Dynamics Simulation Supervised Machine Learning Ligands Cell Membrane
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The Virtual Screening of the Drug Protein with a Few Crystal Structures Based on the Adaboost-SVM.

Computational and mathematical methods in medicine Apr 3, 2016
Using the theory of machine learning to assist the virtual screening (VS) has been an effective plan. However, the quality of the training set may reduce because of mixing with the wrong docking poses and it will affect the screening efficiencies. To...
Humans Software Algorithms Reproducibility of Results Computational Biology Support Vector Machine Models, Statistical Proteins Drug Design ROC Curve Imaging, Three-Dimensional Protein Binding Binding Sites Combinatorial Chemistry Techniques Protein Conformation Chemistry, Pharmaceutical Hydrogen Cathepsin K Databases, Protein Area Under Curve Ligands Crystallization
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A Sequence-Based Dynamic Ensemble Learning System for Protein Ligand-Binding Site Prediction.

IEEE/ACM transactions on computational biology and bioinformatics Dec 3, 2015
BACKGROUND: Proteins have the fundamental ability to selectively bind to other molecules and perform specific functions through such interactions, such as protein-ligand binding. Accurate prediction of protein residues that physically bind to ligands...
Pattern Recognition, Automated Binding Sites Protein Interaction Mapping Sequence Analysis, Protein Machine Learning Algorithms Molecular Docking Simulation Protein Binding Proteins Data Interpretation, Statistical Models, Chemical Ligands
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Ligand-Based Virtual Screening in a Search for Novel Anti-HIV-1 Chemotypes.

Journal of chemical information and modeling Oct 9, 2015
In a search for new anti-HIV-1 chemotypes, we developed a multistep ligand-based virtual screening (VS) protocol combining machine learning (ML) methods with the privileged structures (PS) concept. In its learning step, the VS protocol was based on H...
HIV-1 Ligands Inhibitory Concentration 50 HIV Integrase Inhibitors Molecular Structure Drug Evaluation, Preclinical Biological Assay Humans Machine Learning Cells, Cultured Anti-HIV Agents Models, Molecular
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Neural-Network Scoring Functions Identify Structurally Novel Estrogen-Receptor Ligands.

Journal of chemical information and modeling Sep 4, 2015
The magnitude of the investment required to bring a drug to the market hinders medical progress, requiring hundreds of millions of dollars and years of research and development. Any innovation that improves the efficiency of the drug-discovery proces...
Ligands Drug Discovery Humans Protein Binding Molecular Conformation Neural Networks, Computer Receptors, Estrogen Databases, Factual Estradiol Computer Simulation Models, Biological
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idDock+: Integrating Machine Learning in Probabilistic Search for Protein-Protein Docking.

Journal of computational biology : a journal of computational molecular cell biology Jul 29, 2015
Predicting the three-dimensional native structures of protein dimers, a problem known as protein-protein docking, is key to understanding molecular interactions. Docking is a computationally challenging problem due to the diversity of interactions an...
Protein Binding Computational Biology Proteins Ligands Machine Learning Algorithms Molecular Docking Simulation Protein Conformation Binding Sites Protein Multimerization
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Development of 3D-QSAR Model for Acetylcholinesterase Inhibitors Using a Combination of Fingerprint, Molecular Docking, and Structure-Based Pharmacophore Approaches.

Toxicological sciences : an official journal of the Society of Toxicology Jul 21, 2015
Acetylcholinesterase (AChE), a serine hydrolase vital for regulating the neurotransmitter acetylcholine in animals, has been used as a target for drugs and pesticides. With the increasing availability of AChE crystal structures, with or without ligan...
Artificial Intelligence Cholinesterase Inhibitors Animals Expert Systems Molecular Docking Simulation GPI-Linked Proteins Catalytic Domain Quantitative Structure-Activity Relationship Imaging, Three-Dimensional Insecticides Molecular Conformation Binding Sites Ligands Humans Peptide Mapping Acetylcholinesterase Nootropic Agents Computational Biology Databases, Protein Nerve Tissue Proteins Models, Molecular
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The study of dual COX-2/5-LOX inhibitors by using electronic-topological approach based on data on the ligand-receptor interactions.

Journal of molecular graphics & modelling Jun 19, 2015
Structural and electronic factors influencing selective inhibition of cyclooxygenase-2 and 5-lipoxygenase (COX-2/5-LOX) were studied by using Electronic-Topological Method combined with Neural Networks (ETM-NN), molecular docking, and Density Functio...
Substrate Specificity Quantum Theory Ligands Cyclooxygenase 2 Inhibitors Datasets as Topic Catalytic Domain Arachidonate 5-Lipoxygenase Molecular Docking Simulation Cyclooxygenase 2 Protein Binding Humans Lipoxygenase Inhibitors Structure-Activity Relationship Neural Networks, Computer Molecular Structure Algorithms
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