AIMC Topic: Thermodynamics

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3D matters! 3D-RISM and 3D convolutional neural network for accurate bioaccumulation prediction.

Journal of physics. Condensed matter : an Institute of Physics journal Jul 2, 2018
In this work, we present a new method for predicting complex physical-chemical properties of organic molecules. The approach utilizes 3D convolutional neural network (ActivNet4) that uses solvent spatial distributions around solutes as input. These s...
Models, Molecular Linear Models Molecular Conformation Thermodynamics Neural Networks, Computer
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Perturbation-Theory and Machine Learning (PTML) Model for High-Throughput Screening of Parham Reactions: Experimental and Theoretical Studies.

Journal of chemical information and modeling Jun 27, 2018
Machine learning (ML) algorithms are gaining importance in the processing of chemical information and modeling of chemical reactivity problems. In this work, we have developed a perturbation-theory and machine learning (PTML) model combining perturba...
Linear Models Databases, Chemical Organometallic Compounds Models, Chemical Isoquinolines High-Throughput Screening Assays Thermodynamics Cyclization Neural Networks, Computer Machine Learning Structure-Activity Relationship Molecular Structure Algorithms Lithium
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Computational design of thermostabilizing point mutations for G protein-coupled receptors.

eLife Jun 21, 2018
Engineering of GPCR constructs with improved thermostability is a key for successful structural and biochemical studies of this transmembrane protein family, targeted by 40% of all therapeutic drugs. Here we introduce a comprehensive computational ap...
Protein Engineering Thermodynamics Sequence Alignment Receptor, Serotonin, 5-HT2C Crystallography, X-Ray Binding Sites Protein Conformation, beta-Strand Point Mutation Serotonin 5-HT2 Receptor Agonists Serotonin 5-HT2 Receptor Antagonists Sequence Homology, Amino Acid Protein Interaction Domains and Motifs Protein Conformation, alpha-Helical Protein Binding Models, Molecular Gene Expression Kinetics Amino Acid Sequence Protein Stability Humans Machine Learning Animals
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Development of a machine-learning model to predict Gibbs free energy of binding for protein-ligand complexes.

Biophysical chemistry Jun 7, 2018
The possibility of using the atomic coordinates of protein-ligand complexes to assess binding affinity has a beneficial impact in the early stages of drug development and design. From the computational view, the creation of reliable scoring functions...
Thermodynamics Proteins Databases, Protein Ligands Machine Learning Molecular Docking Simulation Protein Binding
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Reliable and Performant Identification of Low-Energy Conformers in the Gas Phase and Water.

Journal of chemical information and modeling May 16, 2018
Prediction of compound properties from structure via quantitative structure-activity relationship and machine-learning approaches is an important computational chemistry task in small-molecule drug research. Though many such properties are dependent ...
Gases Informatics Thermodynamics Drug Discovery Water Models, Molecular Molecular Conformation Quantitative Structure-Activity Relationship Pharmaceutical Preparations Solvents Machine Learning
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Machine Learning of Partial Charges Derived from High-Quality Quantum-Mechanical Calculations.

Journal of chemical information and modeling Mar 7, 2018
Parametrization of small organic molecules for classical molecular dynamics simulations is not trivial. The vastness of the chemical space makes approaches using building blocks challenging. The most common approach is therefore an individual paramet...
Thermodynamics Volatilization Quantum Theory Electrons Static Electricity Pharmaceutical Preparations Molecular Dynamics Simulation Machine Learning Models, Chemical
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Predicting the Effect of Single and Multiple Mutations on Protein Structural Stability.

Molecules (Basel, Switzerland) Jan 27, 2018
Predicting how a point mutation alters a protein's stability can guide pharmaceutical drug design initiatives which aim to counter the effects of serious diseases. Conducting mutagenesis studies in physical proteins can give insights about the effect...
Protein Conformation Amino Acid Substitution Thermodynamics Proteins Mutation Protein Stability Computer Simulation Support Vector Machine Decision Trees Neural Networks, Computer
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Thermal and Antioxidant Properties of Polysaccharides Sequentially Extracted from Mulberry Leaves (Morus alba L.).

Molecules (Basel, Switzerland) Dec 20, 2017
Polysaccharides from natural plant products are gaining considerable attention due to their multi-faceted health effects, as well their functional applications in food production. We reported the sequential extraction of mulberry leaf polysaccharides...
Monosaccharides Humans Free Radical Scavengers Temperature Hydroxyl Radical Antioxidants Plant Extracts Polysaccharides Plant Leaves Fruit Iron Morus Iron Chelating Agents Thermodynamics
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Effect of the electronegativity on the electrosorption selectivity of anions during capacitive deionization.

Chemosphere Dec 7, 2017
The effect of electronegativity on the electrosorption selectivity of anions during capacitive deionization was investigated via a combination of experimental and theoretical studies. A model was developed based on chemical thermodynamics and the cla...
Electrodes Anions Thermodynamics Water Purification Adsorption Electrochemical Techniques
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Neural Network Based Prediction of Conformational Free Energies - A New Route toward Coarse-Grained Simulation Models.

Journal of chemical theory and computation Nov 28, 2017
Coarse-grained (CG) simulation models have become very popular tools to study complex molecular systems with great computational efficiency on length and time scales that are inaccessible to simulations at atomistic resolution. In so-called bottom-up...
Algorithms Thermodynamics Neural Networks, Computer Molecular Dynamics Simulation
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