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

Showing 51 to 60 of 67 articles

Evaluation of different virtual screening strategies on the basis of compound sets with characteristic core distributions and dissimilarity relationships.

Journal of computer-aided molecular design Aug 21, 2019
In this work, computational compound screening strategies on the basis of two- and three-dimensional (2D and 3D) molecular representations were investigated including similarity searching and support vector machine (SVM) ranking. Calculations based o...
Support Vector Machine Structure-Activity Relationship Molecular Conformation Computational Chemistry Machine Learning User-Computer Interface Protein Binding
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DP-BINDER: machine learning model for prediction of DNA-binding proteins by fusing evolutionary and physicochemical information.

Journal of computer-aided molecular design May 23, 2019
DNA-binding proteins (DBPs) participate in various biological processes including DNA replication, recombination, and repair. In the human genome, about 6-7% of these proteins are utilized for genes encoding. DBPs shape the DNA into a compact structu...
DNA Support Vector Machine Algorithms DNA-Binding Proteins Evolution, Molecular Binding Sites Humans Animals Databases, Protein Machine Learning Position-Specific Scoring Matrices
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Elucidating the druggability of the human proteome with eFindSite.

Journal of computer-aided molecular design Mar 19, 2019
Identifying the viability of protein targets is one of the preliminary steps of drug discovery. Determining the ability of a protein to bind drugs in order to modulate its function, termed the druggability, requires a non-trivial amount of time and r...
Humans Software Serine Proteases Binding Sites 5-Aminolevulinate Synthetase Proteome Proteins Drug Design Supervised Machine Learning Drug Discovery Protein Binding
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Boosted feature selectors: a case study on prediction P-gp inhibitors and substrates.

Journal of computer-aided molecular design Oct 26, 2018
Feature selection is commonly used as a preprocessing step to machine learning for improving learning performance, lowering computational complexity and facilitating model interpretation. This paper proposes the application of boosting feature select...
Machine Learning Algorithms Protein Binding Support Vector Machine Quantitative Structure-Activity Relationship ATP Binding Cassette Transporter, Subfamily B Decision Trees Molecular Structure Ligands
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Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges.

Journal of computer-aided molecular design Aug 16, 2018
Advanced mathematics, such as multiscale weighted colored subgraph and element specific persistent homology, and machine learning including deep neural networks were integrated to construct mathematical deep learning models for pose and binding affin...
Binding Sites Thermodynamics Cathepsins Protein Binding Databases, Protein Protein Kinases Protein Conformation Receptors, Cytoplasmic and Nuclear Ligands Crystallography, X-Ray Computer-Aided Design Drug Design Deep Learning Molecular Docking Simulation
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Convolutional neural network scoring and minimization in the D3R 2017 community challenge.

Journal of computer-aided molecular design Jul 10, 2018
We assess the ability of our convolutional neural network (CNN)-based scoring functions to perform several common tasks in the domain of drug discovery. These include correctly identifying ligand poses near and far from the true binding mode when giv...
Binding Sites Cathepsins Molecular Docking Simulation Drug Discovery Neural Networks, Computer Protein Binding Ligands Algorithms Databases, Protein Protein Conformation Structure-Activity Relationship
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Modern drug design: the implication of using artificial neuronal networks and multiple molecular dynamic simulations.

Journal of computer-aided molecular design Nov 13, 2017
We report the implementation of molecular modeling approaches developed as a part of the 2016 Grand Challenge 2, the blinded competition of computer aided drug design technologies held by the D3R Drug Design Data Resource ( https://drugdesigndata.org...
Ligands Protein Conformation Receptors, Cytoplasmic and Nuclear Binding Sites Drug Design Humans Protein Binding Neural Networks, Computer Molecular Dynamics Simulation Machine Learning Molecular Docking Simulation Computer-Aided Design
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Obituary: Toshio Fujita, QSAR pioneer.

Journal of computer-aided molecular design Nov 8, 2017
This is the obituary for Toshio Fujita, pioneer of the quantitative structure activity relationship (QSAR) paradigm.
Machine Learning Computer-Aided Design Humans Drug Design Quantitative Structure-Activity Relationship Molecular Structure History, 20th Century History, 21st Century
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Convex-PL: a novel knowledge-based potential for protein-ligand interactions deduced from structural databases using convex optimization.

Journal of computer-aided molecular design Sep 18, 2017
We present a novel optimization approach to train a free-shape distance-dependent protein-ligand scoring function called Convex-PL. We do not impose any functional form of the scoring function. Instead, we decompose it into a polynomial basis and ded...
Protein Binding Humans Molecular Structure Protein Conformation Proteins Knowledge Bases Databases, Protein Machine Learning Binding Sites Algorithms Ligands Structure-Activity Relationship Molecular Docking Simulation Drug Design
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Bayesian molecular design with a chemical language model.

Journal of computer-aided molecular design Mar 9, 2017
The aim of computational molecular design is the identification of promising hypothetical molecules with a predefined set of desired properties. We address the issue of accelerating the material discovery with state-of-the-art machine learning techni...
Bayes Theorem Computer-Aided Design Machine Learning Monte Carlo Method Drug Design Models, Chemical Software Small Molecule Libraries Pharmaceutical Preparations Computer Simulation Molecular Structure
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