AIMC Topic: 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 Nucleic Acid Conformation Support Vector Machine DNA
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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 Algorithms Computational Biology Support Vector Machine Sequence Analysis, Protein Position-Specific Scoring Matrices Databases, Protein DNA-Binding Proteins
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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...
Radiographic Image Interpretation, Computer-Assisted DNA-Binding Proteins Reproducibility of Results Kidney Neoplasms Aged Contrast Media Male Predictive Value of Tests Carcinoma, Renal Cell Middle Aged Mutation Nuclear Proteins Retrospective Studies Transcription Factors Tomography, X-Ray Computed Humans Female Machine Learning Algorithms
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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...
Protein Conformation Binding Sites Support Vector Machine DNA DNA-Binding Proteins Humans Machine Learning Algorithms Protein Binding Computational Biology
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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 Databases, Protein DNA Machine Learning Algorithms 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 ...
Algorithms Reproducibility of Results ROC Curve DNA-Binding Proteins Amino Acid Sequence Computational Biology Support Vector Machine
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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...
Neural Networks, Computer Algorithms Animals Protein Binding Mice DNA-Binding Proteins Computational Biology Supervised Machine Learning Transcription Factors Binding Sites DNA
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EL_LSTM: Prediction of DNA-Binding Residue from Protein Sequence by Combining Long Short-Term Memory and Ensemble Learning.

IEEE/ACM transactions on computational biology and bioinformatics Jul 23, 2018
Most past works for DNA-binding residue prediction did not consider the relationships between residues. In this paper, we propose a novel approach for DNA-binding residue prediction, referred to as EL_LSTM, which includes two main components. The fir...
Binding Sites Databases, Protein DNA DNA-Binding Proteins Machine Learning Algorithms Computational Biology
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DPP-PseAAC: A DNA-binding protein prediction model using Chou's general PseAAC.

Journal of theoretical biology May 16, 2018
A DNA-binding protein (DNA-BP) is a protein that can bind and interact with a DNA. Identification of DNA-BPs using experimental methods is expensive as well as time consuming. As such, fast and accurate computational methods are sought for predicting...
Computational Biology Amino Acids Support Vector Machine DNA Databases, Protein DNA-Binding Proteins Models, Molecular Algorithms Amino Acid Sequence Protein Domains Reproducibility of Results Nucleic Acid Conformation
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High-Order Convolutional Neural Network Architecture for Predicting DNA-Protein Binding Sites.

IEEE/ACM transactions on computational biology and bioinformatics Mar 26, 2018
Although Deep learning algorithms have outperformed conventional methods in predicting the sequence specificities of DNA-protein binding, they lack to consider the dependencies among nucleotides and the diverse binding lengths for different transcrip...
Chromatin Immunoprecipitation Transcription Factors Area Under Curve DNA-Binding Proteins Protein Binding Binding Sites Neural Networks, Computer DNA Genomics Amino Acid Motifs Software Computational Biology Algorithms
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