AIMC Topic: DNA-Binding Proteins

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Enabling full-length evolutionary profiles based deep convolutional neural network for predicting DNA-binding proteins from sequence.

Proteins Jul 8, 2019
Sequence based DNA-binding protein (DBP) prediction is a widely studied biological problem. Sliding windows on position specific substitution matrices (PSSMs) rows predict DNA-binding residues well on known DBPs but the same models cannot be applied ...
Animals Mice DNA Humans Neural Networks, Computer Protein Conformation Binding Sites Arabidopsis Proteins Arabidopsis Amino Acids DNA-Binding Proteins Models, Biological
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Modeling in-vivo protein-DNA binding by combining multiple-instance learning with a hybrid deep neural network.

Scientific reports Jun 11, 2019
Modeling in-vivo protein-DNA binding is not only fundamental for further understanding of the regulatory mechanisms, but also a challenging task in computational biology. Deep-learning based methods have succeed in modeling in-vivo protein-DNA bindin...
Models, Biological Protein Binding DNA DNA-Binding Proteins Neural Networks, Computer Humans Algorithms Deep Learning
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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...
Algorithms Animals Support Vector Machine Evolution, Molecular Humans Machine Learning Binding Sites Position-Specific Scoring Matrices Databases, Protein DNA DNA-Binding Proteins
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DNAPred: Accurate Identification of DNA-Binding Sites from Protein Sequence by Ensembled Hyperplane-Distance-Based Support Vector Machines.

Journal of chemical information and modeling Apr 16, 2019
Accurate identification of protein-DNA binding sites is significant for both understanding protein function and drug design. Machine-learning-based methods have been extensively used for the prediction of protein-DNA binding sites. However, the data ...
Models, Molecular DNA-Binding Proteins Protein Conformation Support Vector Machine DNA Nucleic Acid Conformation
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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...
Machine Learning Databases, Protein Position-Specific Scoring Matrices Algorithms DNA-Binding Proteins Computational Biology Sequence Analysis, Protein Support Vector Machine
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Radiogenomics in Clear Cell Renal Cell Carcinoma: Machine Learning-Based High-Dimensional Quantitative CT Texture Analysis in Predicting PBRM1 Mutation Status.

AJR. American journal of roentgenology Jan 2, 2019
OBJECTIVE: The purpose of this study is to evaluate the potential value of machine learning (ML)-based high-dimensional quantitative CT texture analysis in predicting the mutation status of the gene encoding the protein polybromo-1 (PBRM1) in patient...
Carcinoma, Renal Cell Contrast Media Predictive Value of Tests Mutation Radiographic Image Interpretation, Computer-Assisted DNA-Binding Proteins Kidney Neoplasms Middle Aged Humans Machine Learning Nuclear Proteins Tomography, X-Ray Computed Transcription Factors Reproducibility of Results Female Aged Algorithms Male Retrospective Studies
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PDRLGB: precise DNA-binding residue prediction using a light gradient boosting machine.

BMC bioinformatics Dec 31, 2018
BACKGROUND: Identifying specific residues for protein-DNA interactions are of considerable importance to better recognize the binding mechanism of protein-DNA complexes. Despite the fact that many computational DNA-binding residue prediction approach...
Support Vector Machine DNA Algorithms DNA-Binding Proteins Protein Binding Protein Conformation Humans Computational Biology Binding Sites Machine Learning
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Prediction of DNA-Binding Residues in Local Segments of Protein Sequences with Fuzzy Cognitive Maps.

IEEE/ACM transactions on computational biology and bioinformatics Dec 28, 2018
While protein-DNA interactions are crucial for a wide range of cellular functions, only a small fraction of these interactions was annotated to date. One solution to close this annotation gap is to employ computational methods that accurately predict...
DNA-Binding Proteins Fuzzy Logic Machine Learning Databases, Protein Algorithms DNA Computational Biology
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Effective DNA binding protein prediction by using key features via Chou's general PseAAC.

Journal of theoretical biology Oct 11, 2018
DNA-binding proteins (DBPs) are responsible for several cellular functions, starting from our immunity system to the transport of oxygen. In the recent studies, scientists have used supervised machine learning based methods that use information from ...
Support Vector Machine Algorithms DNA-Binding Proteins Reproducibility of Results Amino Acid Sequence ROC Curve Computational Biology
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Weakly-Supervised Convolutional Neural Network Architecture for Predicting Protein-DNA Binding.

IEEE/ACM transactions on computational biology and bioinformatics Aug 7, 2018
Although convolutional neural networks (CNN) have outperformed conventional methods in predicting the sequence specificities of protein-DNA binding in recent years, they do not take full advantage of the intrinsic weakly-supervised information of DNA...
Transcription Factors Protein Binding DNA Mice Neural Networks, Computer Supervised Machine Learning DNA-Binding Proteins Computational Biology Algorithms Binding Sites Animals
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