AIMC Topic: Proteins

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MUFOLD-SS: New deep inception-inside-inception networks for protein secondary structure prediction.

Proteins Mar 12, 2018
Protein secondary structure prediction can provide important information for protein 3D structure prediction and protein functions. Deep learning offers a new opportunity to significantly improve prediction accuracy. In this article, a new deep neura...
Algorithms Deep Learning Protein Binding Software Amino Acid Sequence Binding Sites Protein Structure, Secondary Proteins Models, Molecular Amino Acids
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MetaGO: Predicting Gene Ontology of Non-homologous Proteins Through Low-Resolution Protein Structure Prediction and Protein-Protein Network Mapping.

Journal of molecular biology Mar 10, 2018
Homology-based transferal remains the major approach to computational protein function annotations, but it becomes increasingly unreliable when the sequence identity between query and template decreases below 30%. We propose a novel pipeline, MetaGO,...
Internet Amino Acid Sequence Protein Conformation Computational Biology Proteins Models, Molecular Sequence Analysis, Protein Gene Ontology Protein Interaction Mapping Sequence Homology, Amino Acid Software Algorithms Reproducibility of Results Protein Interaction Maps
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Prediction and characterization of human ageing-related proteins by using machine learning.

Scientific reports Mar 6, 2018
Ageing has a huge impact on human health and economy, but its molecular basis - regulation and mechanism - is still poorly understood. By today, more than three hundred genes (almost all of them function as protein-coding genes) have been related to ...
Humans Machine Learning Gene Regulatory Networks Aging Computational Biology Proteins Protein Interaction Maps
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Deep Learning and Its Applications in Biomedicine.

Genomics, proteomics & bioinformatics Mar 6, 2018
Advances in biological and medical technologies have been providing us explosive volumes of biological and physiological data, such as medical images, electroencephalography, genomic and protein sequences. Learning from these data facilitates the und...
Algorithms Humans Image Interpretation, Computer-Assisted Genomics Computational Biology Protein Structure, Secondary Neural Networks, Computer Proteins Machine Learning Diagnostic Imaging
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Natural language processing in text mining for structural modeling of protein complexes.

BMC bioinformatics Mar 5, 2018
BACKGROUND: Structural modeling of protein-protein interactions produces a large number of putative configurations of the protein complexes. Identification of the near-native models among them is a serious challenge. Publicly available results of bio...
Data Mining Semantics Machine Learning Protein Binding Support Vector Machine Proteins Natural Language Processing Models, Molecular
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Knowledge-Based Conformer Generation Using the Cambridge Structural Database.

Journal of chemical information and modeling Feb 22, 2018
Fast generation of plausible molecular conformations is central to molecular modeling. This paper presents an approach to conformer generation that makes extensive use of the information available in the Cambridge Structural Database. By using geomet...
Software Algorithms Proteins Macrocyclic Compounds Databases, Protein Models, Molecular Hydrogen Bonding Knowledge Bases Ligands Databases, Chemical Molecular Conformation
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Statistical and machine learning approaches to predicting protein-ligand interactions.

Current opinion in structural biology Feb 20, 2018
Data driven computational approaches to predicting protein-ligand binding are currently achieving unprecedented levels of accuracy on held-out test datasets. Up until now, however, this has not led to corresponding breakthroughs in our ability to des...
Proteins Machine Learning Ligands Algorithms Quantitative Structure-Activity Relationship Humans Protein Binding Computational Biology Models, Statistical
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Exploring autophagy with Gene Ontology.

Autophagy Feb 17, 2018
Autophagy is a fundamental cellular process that is well conserved among eukaryotes. It is one of the strategies that cells use to catabolize substances in a controlled way. Autophagy is used for recycling cellular components, responding to cellular ...
Autophagy Molecular Sequence Annotation Humans Databases, Genetic Gene Ontology Animals Parkinson Disease Proteins
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ATPbind: Accurate Protein-ATP Binding Site Prediction by Combining Sequence-Profiling and Structure-Based Comparisons.

Journal of chemical information and modeling Feb 8, 2018
Protein-ATP interactions are ubiquitous in a wide variety of biological processes. Correctly locating ATP binding sites from protein information is an important but challenging task for protein function annotation and drug discovery. However, there i...
Binding Sites Protein Structure, Secondary Databases, Protein Adenosine Triphosphate Solvents Support Vector Machine Proteins
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Exploring the potential of 3D Zernike descriptors and SVM for protein-protein interface prediction.

BMC bioinformatics Feb 6, 2018
BACKGROUND: The correct determination of protein-protein interaction interfaces is important for understanding disease mechanisms and for rational drug design. To date, several computational methods for the prediction of protein interfaces have been ...
Support Vector Machine ROC Curve Proteins Area Under Curve Amino Acids Binding Sites Protein Interaction Domains and Motifs
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