AI Medical Compendium Journal:
Journal of computer-aided molecular design

Showing 41 to 50 of 67 articles

Improving the binding affinity estimations of protein-ligand complexes using machine-learning facilitated force field method.

Journal of computer-aided molecular design Mar 17, 2020
Scoring functions are routinely deployed in structure-based drug design to quantify the potential for protein-ligand (PL) complex formation. Here, we present a new scoring function Bappl+ that is designed to predict the binding affinities of non-meta...
Machine Learning Drug Design Proteins Databases, Protein Quantum Theory Ligands Metals Protein Binding Computational Biology
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A deep learning approach for the blind logP prediction in SAMPL6 challenge.

Journal of computer-aided molecular design Jan 30, 2020
Water octanol partition coefficient serves as a measure for the lipophilicity of a molecule and is important in the field of drug discovery. A novel method for computational prediction of logarithm of partition coefficient (logP) has been developed u...
Models, Chemical Solubility Thermodynamics Deep Learning Water Molecular Structure Octanols Machine Learning Drug Discovery
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Validating the validation: reanalyzing a large-scale comparison of deep learning and machine learning models for bioactivity prediction.

Journal of computer-aided molecular design Jan 20, 2020
Machine learning methods may have the potential to significantly accelerate drug discovery. However, the increasing rate of new methodological approaches being published in the literature raises the fundamental question of how models should be benchm...
Algorithms Computer Simulation Drug Discovery Deep Learning Humans Machine Learning Area Under Curve User-Computer Interface Benchmarking ROC Curve Drug Evaluation, Preclinical Support Vector Machine
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Deep neural network affinity model for BACE inhibitors in D3R Grand Challenge 4.

Journal of computer-aided molecular design Jan 8, 2020
Drug Design Data Resource (D3R) Grand Challenge 4 (GC4) offered a unique opportunity for designing and testing novel methodology for accurate docking and affinity prediction of ligands in an open and blinded manner. We participated in the beta-secret...
Binding Sites Amyloid Precursor Protein Secretases Aspartic Acid Endopeptidases Macrocyclic Compounds Humans Neural Networks, Computer Molecular Docking Simulation Ligands Enzyme Inhibitors Drug Design Protein Binding
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Undersampling: case studies of flaviviral inhibitory activities.

Journal of computer-aided molecular design Nov 26, 2019
Imbalanced datasets, comprising of more inactive compounds relative to the active ones, are a common challenge in ligand-based model building workflows for drug discovery. This is particularly true for neglected tropical diseases since efforts to ide...
Drug Discovery Antiviral Agents Support Vector Machine Humans Flaviviridae Infections West Nile virus Dengue Virus Zika Virus Flaviviridae
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Prediction of P-glycoprotein inhibitors with machine learning classification models and 3D-RISM-KH theory based solvation energy descriptors.

Journal of computer-aided molecular design Nov 19, 2019
Development of novel in silico methods for questing novel PgP inhibitors is crucial for the reversal of multi-drug resistance in cancer therapy. Here, we report machine learning based binary classification schemes to identify the PgP inhibitors from ...
Thermodynamics Small Molecule Libraries Drug Discovery ATP Binding Cassette Transporter, Subfamily B, Member 1 Solvents Humans Machine Learning
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MathDL: mathematical deep learning for D3R Grand Challenge 4.

Journal of computer-aided molecular design Nov 16, 2019
We present the performances of our mathematical deep learning (MathDL) models for D3R Grand Challenge 4 (GC4). This challenge involves pose prediction, affinity ranking, and free energy estimation for beta secretase 1 (BACE) as well as affinity ranki...
Humans Amyloid Precursor Protein Secretases Aspartic Acid Endopeptidases Cathepsins Binding Sites Protein Binding Thermodynamics Ligands Small Molecule Libraries Molecular Docking Simulation Drug Design Deep Learning
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Exploring fragment-based target-specific ranking protocol with machine learning on cathepsin S.

Journal of computer-aided molecular design Nov 15, 2019
Cathepsin S (CatS), a member of cysteine cathepsin proteases, has been well studied due to its significant role in many pathological processes, including arthritis, cancer and cardiovascular diseases. CatS inhibitors have been included in D3R-GC3 for...
Binding Sites Thermodynamics Cathepsins Molecular Docking Simulation Computer-Aided Design Humans Protein Binding Machine Learning Crystallography, X-Ray Protein Conformation Databases, Protein Ligands
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Nonparametric chemical descriptors for the calculation of ligand-biopolymer affinities with machine-learning scoring functions.

Journal of computer-aided molecular design Nov 14, 2019
The computational prediction of ligand-biopolymer affinities is a crucial endeavor in modern drug discovery and one that still poses major challenges. The choice of the appropriate computational method often reveals itself as a trade-off between accu...
Drug Discovery Protein Binding Proteins Humans Databases, Protein Machine Learning Ligands Algorithms
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Computational methods and tools for binding site recognition between proteins and small molecules: from classical geometrical approaches to modern machine learning strategies.

Journal of computer-aided molecular design Oct 18, 2019
In the current "genomic era" the number of identified genes is growing exponentially. However, the biological function of a large number of the corresponding proteins is still unknown. Recognition of small molecule ligands (e.g., substrates, inhibito...
Computational Biology Software Small Molecule Libraries Proteins Drug Design Models, Molecular Sequence Homology Protein Binding Amino Acid Sequence Humans Ligands Artificial Intelligence Protein Conformation Machine Learning
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