AIMC Topic: Protein Folding

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Predicting improved protein conformations with a temporal deep recurrent neural network.

PloS one Sep 4, 2018
Accurate protein structure prediction from amino acid sequence is still an unsolved problem. The most reliable methods centre on template based modelling. However, the accuracy of these models entirely depends on the availability of experimentally re...
Deep Learning Molecular Dynamics Simulation Amino Acid Sequence Neural Networks, Computer Protein Conformation Software Protein Folding Sequence Analysis, Protein Algorithms
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Sequentially distant but structurally similar proteins exhibit fold specific patterns based on their biophysical properties.

Computational biology and chemistry May 16, 2018
The Three-dimensional structure of a protein depends on the interaction between their amino acid residues. These interactions are in turn influenced by various biophysical properties of the amino acids. There are several examples of proteins that sha...
Protein Conformation Protein Folding Proteins Models, Molecular Bayes Theorem Support Vector Machine
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Linking of single-molecule experiments with molecular dynamics simulations by machine learning.

eLife May 3, 2018
Single-molecule experiments and molecular dynamics (MD) simulations are indispensable tools for investigating protein conformational dynamics. The former provide data, such as donor-acceptor distances, whereas the latter give atomistic information, ...
Machine Learning Protein Conformation Single Molecule Imaging Protein Folding Carrier Proteins Molecular Dynamics Simulation Fluorescence Resonance Energy Transfer
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SPIN2: Predicting sequence profiles from protein structures using deep neural networks.

Proteins Mar 25, 2018
Designing protein sequences that can fold into a given structure is a well-known inverse protein-folding problem. One important characteristic to attain for a protein design program is the ability to recover wild-type sequences given their native bac...
Software Proteins Databases, Protein Neural Networks, Computer Protein Folding Models, Molecular Amino Acid Sequence Protein Structure, Secondary
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Automated Planning Enables Complex Protocols on Liquid-Handling Robots.

ACS synthetic biology Mar 5, 2018
Robotic automation in synthetic biology is especially relevant for liquid handling to facilitate complex experiments. However, research tasks that are not highly standardized are still rarely automated in practice. Two main reasons for this are the s...
Osmolar Concentration Automation Green Fluorescent Proteins Protein Folding Mutant Proteins Robotics Hydrogen-Ion Concentration
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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...
Protein Binding Kinetics Molecular Dynamics Simulation Neural Networks, Computer Machine Learning Algorithms Markov Chains Protein Folding
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Enhancing Evolutionary Couplings with Deep Convolutional Neural Networks.

Cell systems Dec 20, 2017
While genes are defined by sequence, in biological systems a protein's function is largely determined by its three-dimensional structure. Evolutionary information embedded within multiple sequence alignments provides a rich source of data for inferri...
Proteins Databases, Protein Models, Molecular Probability Protein Conformation Sequence Alignment Forecasting Humans Protein Folding Animals Neural Networks, Computer Computational Biology Machine Learning Algorithms
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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...
Protein Folding Models, Statistical Sequence Analysis, Protein Proteins Protein Interaction Domains and Motifs Models, Molecular Molecular Dynamics Simulation Algorithms Crystallography, X-Ray Computational Biology Protein Conformation Support Vector Machine Humans Machine Learning
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Assessment of the model refinement category in CASP12.

Proteins Nov 29, 2017
We here report on the assessment of the model refinement predictions submitted to the 12th Experiment on the Critical Assessment of Protein Structure Prediction (CASP12). This is the fifth refinement experiment since CASP8 (2008) and, as with the pre...
Protein Folding Humans Models, Molecular Algorithms Crystallography, X-Ray Machine Learning Sequence Analysis, Protein Computational Biology Protein Conformation Proteins
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Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12.

Proteins Nov 14, 2017
We develop two complementary pipelines, "Zhang-Server" and "QUARK", based on I-TASSER and QUARK pipelines for template-based modeling (TBM) and free modeling (FM), and test them in the CASP12 experiment. The combination of I-TASSER and QUARK successf...
Algorithms Databases, Protein Sequence Analysis, Protein Humans Models, Molecular Computational Biology Machine Learning Crystallography, X-Ray Proteins Protein Conformation Protein Folding Sequence Alignment
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