AIMC Topic: Position-Specific Scoring Matrices

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Analysis and prediction of human acetylation using a cascade classifier based on support vector machine.

BMC bioinformatics Jun 17, 2019
BACKGROUND: Acetylation on lysine is a widespread post-translational modification which is reversible and plays a crucial role in some biological activities. To better understand the mechanism, it is necessary to identify acetylation sites in protein...
Protein Processing, Post-Translational Proteins Databases, Protein Computational Biology Rats Support Vector Machine Molecular Sequence Annotation Gene Ontology Protein Structure, Secondary Position-Specific Scoring Matrices Amino Acid Sequence Acetylation Lysine Humans Animals Mice
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DP-BINDER: machine learning model for prediction of DNA-binding proteins by fusing evolutionary and physicochemical information.

Journal of computer-aided molecular design May 23, 2019
DNA-binding proteins (DBPs) participate in various biological processes including DNA replication, recombination, and repair. In the human genome, about 6-7% of these proteins are utilized for genes encoding. DBPs shape the DNA into a compact structu...
Humans Machine Learning DNA-Binding Proteins Binding Sites Position-Specific Scoring Matrices Evolution, Molecular Algorithms Databases, Protein Animals DNA Support Vector Machine
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Identification of clathrin proteins by incorporating hyperparameter optimization in deep learning and PSSM profiles.

Computer methods and programs in biomedicine May 17, 2019
BACKGROUND AND OBJECTIVES: Clathrin is an adaptor protein that serves as the principal element of the vesicle-coating complex and is important for the membrane cleavage to dispense the invaginated vesicle from the plasma membrane. The functional loss...
Algorithms Reproducibility of Results Sensitivity and Specificity Humans Neural Networks, Computer Software Deep Learning Clathrin Cell Membrane Position-Specific Scoring Matrices
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Prediction of apoptosis protein subcellular localization via heterogeneous features and hierarchical extreme learning machine.

SAR and QSAR in environmental research Feb 26, 2019
Apoptosis is a fundamental process controlling normal tissue homeostasis by regulating a balance between cell proliferation and death. Predicting the subcellular location of apoptosis proteins is very helpful for understanding the mechanism of progra...
Deep Learning Support Vector Machine Amino Acids Quantitative Structure-Activity Relationship Apoptosis Regulatory Proteins Position-Specific Scoring Matrices Humans
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BGFE: A Deep Learning Model for ncRNA-Protein Interaction Predictions Based on Improved Sequence Information.

International journal of molecular sciences Feb 23, 2019
The interactions between ncRNAs and proteins are critical for regulating various cellular processes in organisms, such as gene expression regulations. However, due to limitations, including financial and material consumptions in recent experimental m...
RNA, Untranslated Position-Specific Scoring Matrices Computational Biology Databases, Protein Amino Acid Sequence Software Deep Learning ROC Curve Protein Binding
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TargetDBP: Accurate DNA-Binding Protein Prediction Via Sequence-Based Multi-View Feature Learning.

IEEE/ACM transactions on computational biology and bioinformatics Jan 18, 2019
Accurately identifying DNA-binding proteins (DBPs) from protein sequence information is an important but challenging task for protein function annotations. In this paper, we establish a novel computational method, named TargetDBP, for accurately targ...
Sequence Analysis, Protein Position-Specific Scoring Matrices Machine Learning Support Vector Machine Algorithms Databases, Protein Computational Biology DNA-Binding Proteins
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Covariance Matrix Adaptation for Multiobjective Multiarmed Bandits.

IEEE transactions on neural networks and learning systems Dec 28, 2018
Upper confidence bound (UCB) is a successful multiarmed bandit for regret minimization. The covariance matrix adaptation (CMA) for Pareto UCB (CMA-PUCB) algorithm considers stochastic reward vectors with correlated objectives. We upper bound the cumu...
Clinical Trials as Topic Motor Activity Position-Specific Scoring Matrices Neural Networks, Computer Algorithms Blood Pressure Humans
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Predicting drug-target interactions using Lasso with random forest based on evolutionary information and chemical structure.

Genomics Dec 11, 2018
The identification of drug-target interactions has great significance for pharmaceutical scientific research. Since traditional experimental methods identifying drug-target interactions is costly and time-consuming, the use of machine learning method...
Databases, Protein Receptors, G-Protein-Coupled Protein Conformation Receptors, Cytoplasmic and Nuclear Ion Channels Position-Specific Scoring Matrices Machine Learning Software Drug Development
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Human Splice-Site Prediction with Deep Neural Networks.

Journal of computational biology : a journal of computational molecular cell biology Apr 18, 2018
Accurate splice-site prediction is essential to delineate gene structures from sequence data. Several computational techniques have been applied to create a system to predict canonical splice sites. For classification tasks, deep neural networks (DNN...
Deep Learning Computational Biology Computer Graphics Neural Networks, Computer Software Algorithms Humans RNA Splice Sites Position-Specific Scoring Matrices
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Prediction of Apoptosis Protein's Subcellular Localization by Fusing Two Different Descriptors Based on Evolutionary Information.

Acta biotheoretica Mar 12, 2018
The apoptosis protein has a central role in the development and the homeostasis of an organism. Obtaining information about the subcellular localization of apoptosis protein is very helpful to understand the apoptosis mechanism and the function of th...
Databases, Protein Position-Specific Scoring Matrices Apoptosis Regulatory Proteins Models, Theoretical Subcellular Fractions Humans Biological Evolution Support Vector Machine Algorithms Apoptosis Computational Biology
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