AIMC Topic: Ligands

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DLSSAffinity: protein-ligand binding affinity prediction a deep learning model.

Physical chemistry chemical physics : PCCP May 4, 2022
Evaluating the protein-ligand binding affinity is a substantial part of the computer-aided drug discovery process. Most of the proposed computational methods predict protein-ligand binding affinity using either limited full-length protein 3D structur...
Deep Learning Amino Acid Sequence Ligands Protein Binding Proteins
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Capturing surface complementarity in proteins using unsupervised learning and robust curvature measure.

Proteins Apr 23, 2022
The structure of a protein plays a pivotal role in determining its function. Often, the protein surface's shape and curvature dictate its nature of interaction with other proteins and biomolecules. However, marked by corrugations and roughness, a pro...
Ligands Algorithms Proteins Unsupervised Machine Learning Models, Molecular
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Machine learning approaches and their applications in drug discovery and design.

Chemical biology & drug design Apr 23, 2022
This review is focused on several machine learning approaches used in chemoinformatics. Machine learning approaches provide tools and algorithms to improve drug discovery. Many physicochemical properties of drugs like toxicity, absorption, drug-drug ...
Artificial Intelligence Machine Learning Drug Discovery Ligands Molecular Docking Simulation Drug Design
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Pose Classification Using Three-Dimensional Atomic Structure-Based Neural Networks Applied to Ion Channel-Ligand Docking.

Journal of chemical information and modeling Apr 21, 2022
The identification of promising lead compounds showing pharmacological activities toward a biological target is essential in early stage drug discovery. With the recent increase in available small-molecule databases, virtual high-throughput screening...
Ligands Ion Channels Protein Binding Neural Networks, Computer Molecular Docking Simulation
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Using Big Data Analytics to "Back Engineer" Protein Conformational Selection Mechanisms.

Molecules (Basel, Switzerland) Apr 13, 2022
In the living cells, proteins bind small molecules (or "ligands") through a "conformational selection" mechanism, where a subset of protein structures are capable of binding the small molecules well while most other protein structures are not capable...
Machine Learning Ligands Protein Binding Data Science Protein Conformation Proteins
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Dowker complex based machine learning (DCML) models for protein-ligand binding affinity prediction.

PLoS computational biology Apr 6, 2022
With the great advancements in experimental data, computational power and learning algorithms, artificial intelligence (AI) based drug design has begun to gain momentum recently. AI-based drug design has great promise to revolutionize pharmaceutical ...
Proteins Artificial Intelligence Machine Learning Ligands Protein Binding
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Improving Predictions with a Multitask Convolutional Siamese Network.

Journal of chemical information and modeling Apr 5, 2022
The lead optimization phase of drug discovery refines an initial hit molecule for desired properties, especially potency. Synthesis and experimental testing of the small perturbations during this refinement can be quite costly and time-consuming. Rel...
Entropy Proteins Ligands Neural Networks, Computer Drug Discovery
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Observing Noncovalent Interactions in Experimental Electron Density for Macromolecular Systems: A Novel Perspective for Protein-Ligand Interaction Research.

Journal of chemical information and modeling Mar 29, 2022
We report for the first time the use of experimental electron density (ED) in the Protein Data Bank for modeling of noncovalent interactions (NCIs) for protein-ligand complexes. Our methodology is based on reduced electron density gradient (RDG) theo...
Ligands Macromolecular Substances Artificial Intelligence Databases, Protein Electrons
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Ligand-based approaches to activity prediction for the early stage of structure-activity-relationship progression.

Journal of computer-aided molecular design Mar 29, 2022
The retrospective evaluation of virtual screening approaches and activity prediction models are important for methodological development. However, for fair comparison, evaluation data sets must be carefully prepared. In this research, we compiled str...
Ligands Support Vector Machine Retrospective Studies Structure-Activity Relationship
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Affinity prediction using deep learning based on SMILES input for D3R grand challenge 4.

Journal of computer-aided molecular design Mar 22, 2022
Modern molecular docking comprises the prediction of pose and affinity. Prediction of docking poses is required for affinity prediction when three-dimensional coordinates of the ligand have not been provided. However, a large number of feature engine...
Protein Conformation Binding Sites Thermodynamics Databases, Protein Ligands Proteins Humans Deep Learning Molecular Docking Simulation Protein Binding Drug Design
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