AlphaFold2-aware protein–DNA binding site prediction using graph transformer

A transformer architecture based on BERT and 2D convolutional neural network to identify DNA enhancers from sequence information

(2021) Nguyen Quoc Khanh Le et al.   BRIEFINGS IN BIOINFORMATICS

GraphBind: protein structural context embedded rules learned by hierarchical graph neural networks for recognizing nucleic-acid-binding residues

(2021) Ying Xia et al.   NUCLEIC ACIDS RESEARCH

Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map

(2021) Jianwen Chen et al.   Journal of Cheminformatics

Structure-aware protein-protein interaction site prediction using deep graph convolutional network

(2021) Qianmu Yuan et al.   BIOINFORMATICS

DNAgenie: accurate prediction of DNA-type-specific binding residues in protein sequences

(2021) Jian Zhang et al.   BRIEFINGS IN BIOINFORMATICS

De Novo Molecule Design Through the Molecular Generative Model Conditioned by 3D Information of Protein Binding Sites

(2021) Mingyuan Xu et al.   Journal of Chemical Information and Modeling

Protein–Peptide Binding Site Detection Using 3D Convolutional Neural Networks

(2021) Igor Kozlovskii et al.   Journal of Chemical Information and Modeling

TransformerCPI: Improving compound–protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments

(2020) Lifan Chen et al.   BIOINFORMATICS

DNAPred: Accurate Identification of DNA-Binding Sites from Protein Sequence by Ensembled Hyperplane-Distance-Based Support Vector Machines

(2019) Yi-Heng Zhu et al.   Journal of Chemical Information and Modeling

Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold

(2019) Martin Steinegger et al.   NATURE METHODS

HH-suite3 for fast remote homology detection and deep protein annotation

(2019) Martin Steinegger et al.   BMC BIOINFORMATICS

A deep learning framework to predict binding preference of RNA constituents on protein surface

(2019) Jordy Homing Lam et al.   Nature Communications

Predicting Retrosynthetic Reactions Using Self-Corrected Transformer Neural Networks

(2019) Shuangjia Zheng et al.   Journal of Chemical Information and Modeling

COACH-D: improved protein–ligand binding sites prediction with refined ligand-binding poses through molecular docking

(2018) Qi Wu et al.   NUCLEIC ACIDS RESEARCH

Accurate and sensitive quantification of protein-DNA binding affinity

(2018) Chaitanya Rastogi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improving the prediction of protein–nucleic acids binding residues via multiple sequence profiles and the consensus of complementary methods

(2018) Hong Su et al.   BIOINFORMATICS

Promoter analysis and prediction in the human genome using sequence-based deep learning models

(2018) Ramzan Umarov et al.   BIOINFORMATICS

JAK2-binding long noncoding RNA promotes breast cancer brain metastasis

(2017) Shouyu Wang et al.   JOURNAL OF CLINICAL INVESTIGATION

HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy

(2017) Yumeng Yan et al.   NUCLEIC ACIDS RESEARCH

Uniclust databases of clustered and deeply annotated protein sequences and alignments

(2016) Milot Mirdita et al.   NUCLEIC ACIDS RESEARCH

THOC2 Mutations Implicate mRNA-Export Pathway in X-Linked Intellectual Disability

(2015) Raman Kumar et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Precision-Recall Plot Is More Informative than the ROC Plot When Evaluating Binary Classifiers on Imbalanced Datasets

(2015) Takaya Saito et al.   PLoS One

DNA and RNA Quadruplex-Binding Proteins

(2014) Václav Brázda et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Novel approach for selecting the best predictor for identifying the binding sites in DNA binding proteins

(2013) R. Nagarajan et al.   NUCLEIC ACIDS RESEARCH

DNABind: A hybrid algorithm for structure-based prediction of DNA-binding residues by combining machine learning- and template-based approaches

(2013) Rong Liu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Structure-Based Function Prediction of Uncharacterized Protein Using Binding Sites Comparison

(2013) Janez Konc et al.   PLoS Computational Biology

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

BioLiP: a semi-manually curated database for biologically relevant ligand–protein interactions

(2012) Jianyi Yang et al.   NUCLEIC ACIDS RESEARCH

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function

(2010) H. Zhao et al.   BIOINFORMATICS

Understanding and Predicting Druggability. A High-Throughput Method for Detection of Drug Binding Sites

(2010) Peter Schmidtke et al.   JOURNAL OF MEDICINAL CHEMISTRY

Genomic repertoires of DNA-binding transcription factors across the tree of life

(2010) Varodom Charoensawan et al.   NUCLEIC ACIDS RESEARCH

Protein–DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins

(2008) Shandar Ahmad et al.   NUCLEIC ACIDS RESEARCH

Improving accuracy and efficiency of blind protein-ligand docking by focusing on predicted binding sites

(2008) Dario Ghersi et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS