AIMC Topic: Proteins

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A sparse autoencoder-based deep neural network for protein solvent accessibility and contact number prediction.

BMC bioinformatics Dec 28, 2017
BACKGROUND: Direct prediction of the three-dimensional (3D) structures of proteins from one-dimensional (1D) sequences is a challenging problem. Significant structural characteristics such as solvent accessibility and contact number are essential for...
Machine Learning Algorithms Proteins Models, Molecular Solvents Neural Networks, Computer
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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...
Forecasting Animals Computational Biology Neural Networks, Computer Machine Learning Algorithms Probability Protein Conformation Protein Folding Proteins Databases, Protein Models, Molecular Humans Sequence Alignment
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New Deep Learning Methods for Protein Loop Modeling.

IEEE/ACM transactions on computational biology and bioinformatics Dec 18, 2017
Computational protein structure prediction is a long-standing challenge in bioinformatics. In the process of predicting protein 3D structures, it is common that parts of an experimental structure are missing or parts of a predicted structure need to ...
Algorithms Computational Biology Deep Learning Proteins
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Utilizing knowledge base of amino acids structural neighborhoods to predict protein-protein interaction sites.

BMC bioinformatics Dec 6, 2017
BACKGROUND: Protein-protein interactions (PPI) play a key role in an investigation of various biochemical processes, and their identification is thus of great importance. Although computational prediction of which amino acids take part in a PPI has b...
Databases, Protein Computational Biology Software Protein Interaction Mapping Amino Acids Models, Statistical Proteins Knowledge Bases
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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 Machine Learning Protein Folding Models, Statistical Sequence Analysis, Protein Proteins Algorithms Molecular Dynamics Simulation Protein Interaction Domains and Motifs Models, Molecular Computational Biology Crystallography, X-Ray Support Vector Machine Protein Conformation
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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 Sequence Analysis, Protein Crystallography, X-Ray Protein Conformation Humans Machine Learning Algorithms Computational Biology Proteins Models, Molecular
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isGPT: An optimized model to identify sub-Golgi protein types using SVM and Random Forest based feature selection.

Artificial intelligence in medicine Nov 26, 2017
The Golgi Apparatus (GA) is a key organelle for protein synthesis within the eukaryotic cell. The main task of GA is to modify and sort proteins for transport throughout the cell. Proteins permeate through the GA on the ER (Endoplasmic Reticulum) fac...
Reproducibility of Results Amino Acid Sequence Support Vector Machine Humans Animals Oligopeptides Proteins Computational Biology Golgi Apparatus Databases, Protein
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Computational Intelligence for Medical Imaging Simulations.

Journal of medical systems Nov 25, 2017
This paper describes how to simulate medical imaging by computational intelligence to explore areas that cannot be easily achieved by traditional ways, including genes and proteins simulations related to cancer development and immunity. This paper ha...
Humans Artificial Intelligence Algorithms Diagnostic Imaging Computer Simulation Models, Biological Models, Genetic Models, Immunological Proteins
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Different protein-protein interface patterns predicted by different machine learning methods.

Scientific reports Nov 22, 2017
Different types of protein-protein interactions make different protein-protein interface patterns. Different machine learning methods are suitable to deal with different types of data. Then, is it the same situation that different interface patterns ...
Protein Binding Proteins Analysis of Variance Machine Learning Algorithms
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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...
Humans Machine Learning Algorithms Computational Biology Proteins Databases, Protein Protein Folding Models, Molecular Sequence Alignment Crystallography, X-Ray Sequence Analysis, Protein Protein Conformation
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