Protein-DNA Binding Site Predition

• 中文综述：识别蛋白质配体绑定残基的生物计算方法综述. 数据采集与处理, 2018. [PDF]

• Advancing protein-DNA binding site prediction: integrating sequence models and machine learning classifiers. bioRxiv, 2023. [PDF]

• NABind: Structure-based prediction of nucleic acid binding residues by merging deep learning and template-based approaches. PLoS Computational Biology, 2023. [PDF] [Web Server] [Code]

• ULDNA: Integrating unsupervised multi-source language models with LSTM-attention network for protein-DNA binding site prediction. bioRxiv, 2023. [PDF] [Web Server]

• CLAPE: Protein-DNA binding sites prediction based on pre-trained protein language model and contrastive learning. bioRxiv, 2023. [PDF] [Code]

• GLMSite: Accurately identifying nucleic-acid-binding sites through geometric graph learning on language model predicted structures. bioRxiv, 2023. [PDF] [Code]

• EquiPNAS: Improved protein-nucleic acid binding site prediction using protein-language-model-informed equivariant deep graph neural networks. bioRxiv, 2023. [PDF] [Code]

• ScanNet: An interpretable geometric deep learning model for structure-based protein binding site prediction. Nature Methods, 2022. [PDF] [Web Server]

• PredDBR: Protein-DNA binding residue prediction via bagging strategy and sequence-based cube-format feature. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2022. [PDF] [Web Server]

• DBpred: A deep learning-based method for the prediction of DNA interacting residues in a protein. Briefings in Bioinformatics, 2022. [PDF] [Web Server]

• Guan's Method: Protein-DNA binding residues prediction using a deep learning model with hierarchical feature extraction. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2022. [PDF] [Code]

• GraphSite: AlphaFold2-aware protein-DNA binding site prediction using graph transformer. Briefings in Bioinformatics, 2022. [PDF] [Web Server] [Code]

• DeepDISOBind: Accurate prediction of RNA-, DNA- and protein-binding intrinsically disordered residues with deep multi-task learning. Briefings in Bioinformatics, 2022. [PDF] [Web Server]

• BindWeb: A web server for ligand binding residue and pocket prediction from protein structures. Protein Science, 2022. [PDF] [Web Server]

• iDRNA-ITF: Identifying DNA- and RNA-binding residues in proteins based on induction and transfer framework. Briefings in Bioinformatics, 2022. [PDF] [Web Server]

• NCBRPred: Predicting nucleic acid binding residues in proteins based on multilabel learning. Briefings in Bioinformatics, 2021. [PDF] [Web Server]

• GraphBind: Protein structural context embedded rules learned by hierarchical graph neural networks for recognizing nucleic-acid-binding residues. Nucleic Acids Research, 2021. [PDF] [Web Server]

• DNAgenie: Accurate prediction of DNA-type-specific binding residues in protein sequences. Briefings in Bioinformatics, 2021. [PDF] [Web Server]

• ProNA2020 predicts protein-DNA, protein-RNA, and protein-protein binding proteins and residues from sequence. Journal of Molecular Biology, 2020. [PDF] [Web Server] [Code]

• DNAPred: Accurate identification of DNA-binding sites from protein sequence by ensembled hyperplane-distance-based support vector machines. Journal of Chemical Information and Modeling, 2019. [PDF] [Web Server]

• NUCBind: Improving the prediction of protein-nucleic acids binding residues via multiple sequence profiles and the consensus of complementary methods. Bioinformatics, 2019. [PDF] [Web Server]

• iProDNA-CapsNet: Identifying protein-DNA binding residues using capsule neural networks. BMC Bioinformatics, 2019. [PDF] [Code]

• HybridNAP: Comprehensive review and empirical analysis of hallmarks of DNA-, RNA- and protein-binding residues in protein chains. Briefings in Bioinformatics, 2019. [PDF] [Web Server]

• funDNApred: Prediction of DNA-binding residues in local segments of protein sequences with fuzzy cognitive maps. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2018. [PDF] [Web Server]

• EC-RUS: Identification of Protein−Ligand Binding Sites by Sequence Information and Ensemble Classifier. Journal of Chemical Information and Modeling, 2017. [PDF] [Code]

• TargetDNA: Predicting protein-DNA binding residues by weightedly combining sequence-based features and boosting multiple SVMs. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2016. [PDF] [Web Server]

• CNNsite: Prediction of DNA-binding residues in proteins using convolutional neural network with sequence features. IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2016. [PDF]

• PDNAsite: Identification of DNA-binding site from protein sequence by incorporating spatial and sequence context. Scientific Reports, 2016. [PDF]

• SPOT-Seq(DNA): Predicting DNA-binding proteins and binding residues by complex structure prediction and application to human proteome. PLOS One, 2014. [PDF]

• DNABind: A hybrid algorithm for structure-based prediction of DNA-binding residues by combining machine learning- and template-based approaches. Proteins, 2013. [PDF] [Web Server]

• PreDNA: Accurate prediction of DNA-binding sites in proteins by integrating sequence and geometric structure. Bioinformatics, 2013. [PDF]

• COACH: Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment. Bioinformatics, 2013. [PDF] [Web Server]

• TargetS: Designing template-free predictor for targeting protein-ligand binding sites with classifier ensemble and spatial clustering. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2013. [PDF] [Web Server]

• DNABR: Sequence-based prediction of DNA-binding residues in proteins with conservation and correlation information. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2012. [PDF]

• MetaDBSite: A meta approach to improve protein DNA-binding sites prediction. BMC Systems Biology, 2011. [PDF]

• BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features. BMC Systems Biology, 2010. [PDF]

• DBindR: Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature. Bioinformatics, 2009. [PDF]

• ProteDNA: A sequence-based predictor of sequence-specific DNA-binding residues in transcription factors. Nucleic Acids Research, 2009. [PDF]

• BindN-RF: Prediction of DNA-binding residues from protein sequence information using random forests. BMC Bioinformatics, 2009. [PDF]

• DP-Bind: A web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins. Bioinformatics, 2007. [PDF] [Web Server]

• DNABindR: Predicting DNA-binding sites of proteins from amino acid sequence. BMC Bioinformatics, 2006. [PDF]

• BindN: A web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences. Nucleic Acids Research, 2006. [PDF]

• Pro-DNA: Structure based prediction of binding residues on DNA-binding proteins. IEEE Engineering in Medicine and Biology 27th Annual Conference, 2005. [PDF]

• DBS-PSSM: PSSM-based prediction of DNA binding sites in proteins. BMC Bioinformatics, 2005. [PDF]

• DBS-Pred: Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information. Bioinformatics, 2004. [PDF]