AIMC Topic: Molecular Dynamics Simulation

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Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening.

PLoS computational biology Jan 8, 2018
This work introduces a number of algebraic topology approaches, including multi-component persistent homology, multi-level persistent homology, and electrostatic persistence for the representation, characterization, and description of small molecules...
Ligands Nucleic Acids Static Electricity Protein Interaction Mapping Databases, Protein Area Under Curve Molecular Dynamics Simulation Neural Networks, Computer Machine Learning Algorithms Protein Binding Computational Biology Models, Neurological Proteins Humans
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VAMPnets for deep learning of molecular kinetics.

Nature communications Jan 2, 2018
There is an increasing demand for computing the relevant structures, equilibria, and long-timescale kinetics of biomolecular processes, such as protein-drug binding, from high-throughput molecular dynamics simulations. Current methods employ transfor...
Kinetics Molecular Dynamics Simulation Markov Chains Protein Folding Neural Networks, Computer Machine Learning Algorithms Protein Binding
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Carboxybetaine-modified succinylated chitosan-based beads encourage pancreatic β-cells (Min-6) to form islet-like spheroids under in vitro conditions.

Journal of materials science. Materials in medicine Dec 30, 2017
In vitro, pancreatic β-cells tend to reduce their ability to aggregate into islets and lose insulin-producing ability, likely due to insufficient cell-cell and cell-matrix interactions that are essential for β-cell retention, viability and functional...
Homeodomain Proteins Microscopy, Fluorescence Scattering, Radiation Insulin-Secreting Cells Cadherins Spheroids, Cellular Animals Spectroscopy, Fourier Transform Infrared Insulin Secretion Molecular Dynamics Simulation Trans-Activators Cell Culture Techniques Insulin Carbon Lasers Betaine Mice Cell Survival Microscopy, Electron, Scanning Chitosan Surface Properties
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Protein structure modeling and refinement by global optimization in CASP12.

Proteins Dec 5, 2017
For protein structure modeling in the CASP12 experiment, we have developed a new protocol based on our previous CASP11 approach. The global optimization method of conformational space annealing (CSA) was applied to 3 stages of modeling: multiple sequ...
Humans Support Vector Machine Models, Statistical Proteins Models, Molecular Machine Learning Algorithms Computational Biology Protein Folding Sequence Analysis, Protein Molecular Dynamics Simulation Protein Interaction Domains and Motifs Crystallography, X-Ray Protein Conformation
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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 Molecular Dynamics Simulation Thermodynamics Neural Networks, Computer
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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...
Receptors, Cytoplasmic and Nuclear Binding Sites Molecular Docking Simulation Computer-Aided Design Drug Design Protein Binding Molecular Dynamics Simulation Ligands Protein Conformation Humans Neural Networks, Computer Machine Learning
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Simultaneous refinement of inaccurate local regions and overall structure in the CASP12 protein model refinement experiment.

Proteins Oct 26, 2017
Advances in protein model refinement techniques are required as diverse sources of protein structure information are available from low-resolution experiments or informatics-based computations such as cryo-EM, NMR, homology models, or predicted resid...
Protein Interaction Domains and Motifs Humans Machine Learning Algorithms Molecular Dynamics Simulation Computational Biology Crystallography, X-Ray Proteins Protein Conformation Models, Molecular Sequence Analysis, Protein
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The Thermodynamic Basis of the Fuzzy Interaction of an Intrinsically Disordered Protein.

Angewandte Chemie (International ed. in English) Oct 10, 2017
Many intrinsically disordered proteins (IDP) that fold upon binding retain conformational heterogeneity in IDP-target complexes. The thermodynamics of such fuzzy interactions is poorly understood. Herein we introduce a thermodynamic framework, based ...
Protein Binding Fuzzy Logic Models, Molecular Circular Dichroism Kinetics Molecular Dynamics Simulation Amino Acid Sequence Thermodynamics Intrinsically Disordered Proteins Protein Folding Calorimetry
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TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions.

PLoS computational biology Jul 27, 2017
UNLABELLED: Although deep learning approaches have had tremendous success in image, video and audio processing, computer vision, and speech recognition, their applications to three-dimensional (3D) biomolecular structural data sets have been hindered...
Membrane Proteins Models, Statistical Molecular Dynamics Simulation Protein Folding Machine Learning Image Processing, Computer-Assisted Protein Binding Computational Biology Neural Networks, Computer
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Machine Learning and Network Analysis of Molecular Dynamics Trajectories Reveal Two Chains of Red/Ox-specific Residue Interactions in Human Protein Disulfide Isomerase.

Scientific reports Jun 16, 2017
The human protein disulfide isomerase (hPDI), is an essential four-domain multifunctional enzyme. As a result of disulfide shuffling in its terminal domains, hPDI exists in two oxidation states with different conformational preferences which are impo...
Protein Disulfide-Isomerases Oxidation-Reduction Molecular Dynamics Simulation Protein Interaction Domains and Motifs Protein Conformation Protein Interaction Mapping Humans Machine Learning Protein Interaction Maps
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