AIMC Topic: DNA-Binding Proteins

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Transfer String Kernel for Cross-Context DNA-Protein Binding Prediction.

IEEE/ACM transactions on computational biology and bioinformatics Sep 15, 2016
Through sequence-based classification, this paper tries to accurately predict the DNA binding sites of transcription factors (TFs) in an unannotated cellular context. Related methods in the literature fail to perform such predictions accurately, sinc...
DNA-Binding Proteins Animals Protein Binding Mice Computational Biology Models, Statistical Humans DNA Machine Learning Algorithms
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gDNA-Prot: Predict DNA-binding proteins by employing support vector machine and a novel numerical characterization of protein sequence.

Journal of theoretical biology Jul 1, 2016
DNA-binding proteins are the functional proteins in cells, which play an important role in various essential biological activities. An effective and fast computational method gDNA-Prot is proposed to predict DNA-binding proteins in this paper, which ...
Databases, Protein Principal Component Analysis DNA Models, Molecular Protein Domains DNA-Binding Proteins ROC Curve Computational Biology Support Vector Machine Amino Acid Sequence Genome Numerical Analysis, Computer-Assisted
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DNA-binding protein prediction using plant specific support vector machines: validation and application of a new genome annotation tool.

Nucleic acids research Aug 24, 2015
There are currently 151 plants with draft genomes available but levels of functional annotation for putative protein products are low. Therefore, accurate computational predictions are essential to annotate genomes in the first instance, and to provi...
Genome, Plant Support Vector Machine Sequence Analysis, Protein Arabidopsis Plant Proteins Solanum lycopersicum Species Specificity DNA-Binding Proteins Models, Biological Molecular Sequence Annotation
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Identifying DNA-binding proteins by combining support vector machine and PSSM distance transformation.

BMC systems biology Feb 6, 2015
BACKGROUND: DNA-binding proteins play a pivotal role in various intra- and extra-cellular activities ranging from DNA replication to gene expression control. Identification of DNA-binding proteins is one of the major challenges in the field of genome...
Amino Acid Sequence Models, Molecular Protein Conformation Internet Nucleic Acid Conformation Computational Biology DNA-Binding Proteins Molecular Sequence Data Support Vector Machine Sequence Analysis, Protein
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PseDNA-Pro: DNA-Binding Protein Identification by Combining Chou's PseAAC and Physicochemical Distance Transformation.

Molecular informatics Sep 26, 2014
Identification of DNA-binding proteins is an important problem in biomedical research as DNA-binding proteins are crucial for various cellular processes. Currently, the machine learning methods achieve the-state-of-the-art performance with different ...
DNA-Binding Proteins Sequence Analysis, Protein Animals Support Vector Machine Databases, Protein Humans
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BindUP-Alpha: A Webserver for Predicting DNA-and RNA-binding Proteins based on Experimental and Computational Structural Models☆.

Journal of molecular biology Sep 1, 2025
Structural data provides important information on the proteins' function. Recent development of advanced machine learning and artificial intelligence tools, such as AlphaFold, have led to an explosion of predicted protein structures. However, many of...
Algorithms Protein Binding Computational Biology Internet RNA-Binding Proteins Software DNA-Binding Proteins Support Vector Machine Protein Conformation Models, Molecular
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DRBP-EDP: classification of DNA-binding proteins and RNA-binding proteins using ESM-2 and dual-path neural network.

NAR genomics and bioinformatics Jun 1, 2025
Regulation of DNA or RNA at the transcriptional, post-transcriptional, and translational levels are key steps in the central dogma of molecular biology. DNA-binding proteins (DBPs) and RNA-binding proteins (RBPs) play pivotal roles in the precise reg...
Databases, Protein DNA-Binding Proteins Humans Software Neural Networks, Computer Deep Learning RNA-Binding Proteins
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PLM-DBPs: enhancing plant DNA-binding protein prediction by integrating sequence-based and structure-aware protein language models.

Briefings in bioinformatics May 1, 2025
DNA-binding proteins (DBPs) play a crucial role in gene regulation, development, and environmental responses across plants, animals, and microorganisms. Existing DBP prediction methods are largely limited to sequence information, whether through hand...
Plant Proteins Computational Biology DNA-Binding Proteins Plants Deep Learning
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iProtDNA-SMOTE: Enhancing protein-DNA binding sites prediction through imbalanced graph neural networks.

PloS one Jan 1, 2025
Protein-DNA interactions play a crucial role in cellular biology, essential for maintaining life processes and regulating cellular functions. We propose a method called iProtDNA-SMOTE, which utilizes non-equilibrium graph neural networks along with p...
Neural Networks, Computer Software Databases, Protein DNA DNA-Binding Proteins Algorithms Protein Binding Computational Biology Binding Sites Graph Neural Networks
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Screening of gastric cancer diagnostic biomarkers in the homologous recombination signaling pathway and assessment of their clinical and radiomic correlations.

Cancer medicine Aug 1, 2024
BACKGROUND: Homologous recombination plays a vital role in the occurrence and drug resistance of gastric cancer. This study aimed to screen new gastric cancer diagnostic biomarkers in the homologous recombination pathway and then used radiomic featur...
Homologous Recombination Signal Transduction Neoplasm Staging DNA-Binding Proteins Stomach Neoplasms Radiomics Biomarkers, Tumor Male Middle Aged Gene Expression Regulation, Neoplastic Tomography, X-Ray Computed Female Aged Humans Machine Learning
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