AIMC Topic: Proteins

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Uncertainty, imprecision, and many-valued logics in protein bioinformatics.

Mathematical biosciences Aug 14, 2018
Understanding proteins, their structures, functions, mutual interactions, activity in cellular reactions, interactions with drugs, and expression in body cells is a key to efficient medical diagnosis, drug production, and treatment of patients. Machi...
Fuzzy Logic Proteins Uncertainty Big Data Computational Biology
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PROSES: A Web Server for Sequence-Based Protein Encoding.

Journal of computational biology : a journal of computational molecular cell biology Jul 27, 2018
Recently, the number of the amino acid sequences shared in online databases is growing rapidly in huge amounts. By using sequence-derived features, machine learning algorithms are successfully applied to prediction of protein functional classes, prot...
Humans Machine Learning Proteins Internet Sequence Analysis, Protein Algorithms Protein Interaction Maps Computational Biology
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SVM-SulfoSite: A support vector machine based predictor for sulfenylation sites.

Scientific reports Jul 26, 2018
Protein S-sulfenylation, which results from oxidation of free thiols on cysteine residues, has recently emerged as an important post-translational modification that regulates the structure and function of proteins involved in a variety of physiologic...
Oxidation-Reduction Sulfhydryl Compounds Cysteine Support Vector Machine Protein Processing, Post-Translational Proteins ROC Curve Computational Biology
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Automatic extraction of protein-protein interactions using grammatical relationship graph.

BMC medical informatics and decision making Jul 23, 2018
BACKGROUND: Relationships between bio-entities (genes, proteins, diseases, etc.) constitute a significant part of our knowledge. Most of this information is documented as unstructured text in different forms, such as books, articles and on-line pages...
Information Storage and Retrieval Proteins Natural Language Processing Algorithms Databases, Factual
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De novo profile generation based on sequence context specificity with the long short-term memory network.

BMC bioinformatics Jul 18, 2018
BACKGROUND: Long short-term memory (LSTM) is one of the most attractive deep learning methods to learn time series or contexts of input data. Increasing studies, including biological sequence analyses in bioinformatics, utilize this architecture. Ami...
Proteins Amino Acid Sequence Databases as Topic ROC Curve Computational Biology Neural Networks, Computer Deep Learning Sequence Homology, Amino Acid
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Protein Secondary Structure Prediction Based on Data Partition and Semi-Random Subspace Method.

Scientific reports Jun 29, 2018
Protein secondary structure prediction is one of the most important and challenging problems in bioinformatics. Machine learning techniques have been applied to solve the problem and have gained substantial success in this research area. However ther...
Humans Neural Networks, Computer Proteins Machine Learning Databases, Protein Algorithms Protein Structure, Secondary Computational Biology
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An in-silico method for identifying aggregation rate enhancer and mitigator mutations in proteins.

International journal of biological macromolecules Jun 24, 2018
Newly synthesized polypeptides must pass stringent quality controls in cells to ensure appropriate folding and function. However, mutations, environmental stresses and aging can reduce efficiencies of these controls, leading to accumulation of protei...
Protein Structure, Secondary Proteins Algorithms Amino Acid Substitution Support Vector Machine Mutation, Missense
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Multi-Factored Gene-Gene Proximity Measures Exploiting Biological Knowledge Extracted from Gene Ontology: Application in Gene Clustering.

IEEE/ACM transactions on computational biology and bioinformatics Jun 21, 2018
To describe the cellular functions of proteins and genes, a potential dynamic vocabulary is Gene Ontology (GO), which comprises of three sub-ontologies namely, Biological-process, Cellular-component, and Molecular-function. It has several application...
Genes Cluster Analysis Multigene Family Animals Molecular Sequence Annotation Proteins Semantics Humans Mice Gene Ontology Yeasts Algorithms Computational Biology
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Visualizing convolutional neural network protein-ligand scoring.

Journal of molecular graphics & modelling Jun 18, 2018
Protein-ligand scoring is an important step in a structure-based drug design pipeline. Selecting a correct binding pose and predicting the binding affinity of a protein-ligand complex enables effective virtual screening. Machine learning techniques c...
Neural Networks, Computer Algorithms Deep Learning ROC Curve Models, Molecular Ligands Protein Binding Molecular Conformation Proteins
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PrESOgenesis: A two-layer multi-label predictor for identifying fertility-related proteins using support vector machine and pseudo amino acid composition approach.

Scientific reports Jun 13, 2018
Successful spermatogenesis and oogenesis are the two genetically independent processes preceding embryo development. To date, several fertility-related proteins have been described in mammalian species. Nevertheless, further studies are required to d...
Fertility Spermatogenesis Oogenesis Support Vector Machine Proteins Amino Acids Male Computational Biology Humans Software Algorithms Female Reproducibility of Results Animals
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