Protein embeddings and deep learning predict binding residues for various ligand classes.
Sign Up to like & getrecommendations! Published in 2021 at "Scientific reports"
DOI: 10.1038/s41598-021-03431-4
Abstract: One important aspect of protein function is the binding of proteins to ligands, including small molecules, metal ions, and macromolecules such as DNA or RNA. Despite decades of experimental progress many binding sites remain obscure.… read more here.
Keywords: ligand classes; embeddings deep; binding residues; small molecules ... See more keywords
DNAgenie: accurate prediction of DNA-type-specific binding residues in protein sequences.
Sign Up to like & getrecommendations! Published in 2021 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbab336
Abstract: Efforts to elucidate protein-DNA interactions at the molecular level rely in part on accurate predictions of DNA-binding residues in protein sequences. While there are over a dozen computational predictors of the DNA-binding residues, they are… read more here.
Keywords: binding residues; dna; dna type; protein sequences ... See more keywords
iDRNA-ITF: identifying DNA- and RNA-binding residues in proteins based on induction and transfer framework
Sign Up to like & getrecommendations! Published in 2022 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbac236
Abstract: Protein-DNA and protein-RNA interactions are involved in many biological activities. In the post-genome era, accurate identification of DNA- and RNA-binding residues in protein sequences is of great significance for studying protein functions and promoting new… read more here.
Keywords: idrna itf; binding residues; rna binding; dna ... See more keywords
TSNAPred: predicting type-specific nucleic acid binding residues via an ensemble approach
Sign Up to like & getrecommendations! Published in 2022 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbac244
Abstract: MOTIVATION The interplay between protein and nucleic acid participates in diverse biological activities. Accurately identifying the interaction between protein and nucleic acid can strengthen the understanding of protein function. However, conventional methods are too time-consuming,… read more here.
Keywords: acid binding; type specific; specific nucleic; acid ... See more keywords
Prediction of protein-binding residues: dichotomy of sequence-based methods developed using structured complexes versus disordered proteins
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DOI: 10.1093/bioinformatics/btaa573
Abstract: MOTIVATION There are over 30 sequence-based predictors of the protein-binding residues (PBRs). They use either structure-annotated or disorder-annotated training datasets, potentially creating a dichotomy where the structure-/disorder-specific models may not be able to cross-over to… read more here.
Keywords: protein binding; binding residues; disorder; sequence based ... See more keywords
Predicting protein-peptide binding residues via interpretable deep learning
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DOI: 10.1093/bioinformatics/btac352
Abstract: AVAILABILITY Identifying the protein-peptide binding residues is fundamentally important to understand the mechanisms of protein functions and explore drug discovery. Although several computational methods have been developed, they highly rely on third-party tools or information… read more here.
Keywords: protein peptide; peptide binding; pepbcl; deep learning ... See more keywords
Prediction of DNA-Binding Residues in Local Segments of Protein Sequences with Fuzzy Cognitive Maps
Sign Up to like & getrecommendations! Published in 2020 at "IEEE/ACM Transactions on Computational Biology and Bioinformatics"
DOI: 10.1109/tcbb.2018.2890261
Abstract: 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… read more here.
Keywords: binding residues; dna binding; mml; mml mml ... See more keywords
Protein-DNA Binding Residue Prediction via Bagging Strategy and Sequence-based Cube-Format Feature.
Sign Up to like & getrecommendations! Published in 2021 at "IEEE/ACM transactions on computational biology and bioinformatics"
DOI: 10.1109/tcbb.2021.3123828
Abstract: Protein-DNA interactions play an important role in biological processes. Accurately identifying DNA-binding residues is a critical but challenging task for protein function annotations and drug design. Although wet-lab experimental methods are the most accurate way… read more here.
Keywords: binding residues; dna binding; dna; protein dna ... See more keywords
SCAMPER: Accurate Type-Specific Prediction of Calcium-Binding Residues Using Sequence-Derived Features
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DOI: 10.1109/tcbb.2022.3173437
Abstract: Understanding molecular mechanisms involved in calcium-protein interactions and modeling corresponding docking rely on the accurate identification of calcium-binding residues (CaBRs). The defects of experimentally annotating protein functions enhances the development of computational approaches that correctly… read more here.
Keywords: scamper accurate; calcium binding; calcium; binding residues ... See more keywords
Protein-DNA Binding Residues Prediction Using a Deep Learning Model with Hierarchical Feature Extraction.
Sign Up to like & getrecommendations! Published in 2022 at "IEEE/ACM transactions on computational biology and bioinformatics"
DOI: 10.1109/tcbb.2022.3190933
Abstract: Biologically important effects occur when proteins bind to other substances, of which binding to DNA is a crucial one. Therefore, accurate identification of protein-DNA binding residues is important for further understanding of the protein-DNA interaction… read more here.
Keywords: dna; feature; protein dna; model ... See more keywords
GraphPLBR: Protein-ligand Binding Residue Prediction with Deep Graph Convolution Network.
Sign Up to like & getrecommendations! Published in 2023 at "IEEE/ACM transactions on computational biology and bioinformatics"
DOI: 10.1109/tcbb.2023.3239983
Abstract: The intermolecular interactions between proteins and ligands occur through site-specific amino acid residues in the proteins, and the identification of these key residues plays a critical role in both interpreting protein function and facilitating drug… read more here.
Keywords: deep graph; ligand binding; prediction; binding residues ... See more keywords