DeepDISOBind: accurate prediction of RNA-, DNA- and protein-binding intrinsically disordered residues with deep multi-task learning

DeepDist: real-value inter-residue distance prediction with deep residual convolutional network

(2021) Tianqi Wu et al.   BMC BIOINFORMATICS

Critical assessment of protein intrinsic disorder prediction

(2021) Marco Necci et al.   NATURE METHODS

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

(2021) Qianmu Yuan et al.   BIOINFORMATICS

Compositional framework for multitask learning in the identification of cleavage sites of HIV-1 protease

(2020) Deepak Singh et al.   JOURNAL OF BIOMEDICAL INFORMATICS

ProNA2020 predicts protein-DNA, protein-RNA and protein-protein binding proteins and residues from sequence

(2020) Jiajun Qiu et al.   JOURNAL OF MOLECULAR BIOLOGY

Prediction of protein-binding residues: dichotomy of sequence-based methods developed using structured complexes vs. disordered proteins

(2020) Jian Zhang et al.   BIOINFORMATICS

Graph-based prediction of Protein-protein interactions with attributed signed graph embedding

(2020) Fang Yang et al.   BMC BIOINFORMATICS

Understanding COVID-19 via comparative analysis of dark proteomes of SARS-CoV-2, human SARS and bat SARS-like coronaviruses

(2020) Rajanish Giri et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

PSIONplusm Server for Accurate Multi-Label Prediction of Ion Channels and Their Types

(2020) Jianzhao Gao et al.   Biomolecules

Comprehensive Survey and Comparative Assessment of RNA-Binding Residue Predictions with Analysis by RNA Type

(2020) Kui Wang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

PROBselect: accurate prediction of protein-binding residues from proteins sequences via dynamic predictor selection

(2020) Fuhao Zhang et al.   BIOINFORMATICS

NCBRPred: predicting nucleic acid binding residues in proteins based on multilabel learning

(2020) Jun Zhang et al.   BRIEFINGS IN BIOINFORMATICS

Comparative Assessment of Intrinsic Disorder Predictions with a Focus on Protein and Nucleic Acid-Binding Proteins

(2020) Akila Katuwawala et al.   Biomolecules

A Deep Learning Framework for Gene Ontology Annotations With Sequence- and Network-Based Information

(2020) Fuhao Zhang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Computational Prediction of MoRFs, Short Disorder-to-order Transitioning Protein Binding Regions

(2019) Akila Katuwawala et al.   Computational and Structural Biotechnology Journal

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

SCRIBER: accurate and partner type-specific prediction of protein-binding residues from proteins sequences

(2019) Jian Zhang et al.   BIOINFORMATICS

DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites

(2019) Fuyi Li et al.   BIOINFORMATICS

Alignment-Free Method to Predict Enzyme Classes and Subclasses

(2019) Riccardo Concu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

ImPLoc: a multi-instance deep learning model for the prediction of protein subcellular localization based on immunohistochemistry images

(2019) Wei Long et al.   BIOINFORMATICS

iProDNA-CapsNet: identifying protein-DNA binding residues using capsule neural networks

(2019) Binh P. Nguyen et al.   BMC BIOINFORMATICS

Automated ICD-9 Coding via A Deep Learning Approach

(2018) Min Li et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

The Disordered C-Terminus of Yeast Hsf1 Contains a Cryptic Low-Complexity Amyloidogenic Region

(2018) Jordi Pujols et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The FCS-like zinc finger scaffold of the kinase SnRK1 is formed by the coordinated actions of the FLZ domain and intrinsically disordered regions

(2018) Muhammed Jamsheer K et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding

(2018) Bálint Mészáros et al.   NUCLEIC ACIDS RESEARCH

In Silico Prediction and Validation of Novel RNA Binding Proteins and Residues in the Human Proteome

(2018) Shomeek Chowdhury et al.   PROTEOMICS

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

AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors

(2018) Hui Hu et al.   NUCLEIC ACIDS RESEARCH

Protein–protein interaction sites prediction by ensemble random forests with synthetic minority oversampling technique

(2018) Xiaoying Wang et al.   BIOINFORMATICS

Disordered Regions of Mixed Lineage Leukemia 4 (MLL4) Protein Are Capable of RNA Binding

(2018) Beáta Szabó et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Accurate Single-Sequence Prediction of Protein Intrinsic Disorder by an Ensemble of Deep Recurrent and Convolutional Architectures

(2018) Jack Hanson et al.   Journal of Chemical Information and Modeling

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

OPAL+: Length-Specific MoRF Prediction in Intrinsically Disordered Protein Sequences

(2018) Ronesh Sharma et al.   PROTEOMICS

Identifying Short Disorder-to-Order Binding Regions in Disordered Proteins with a Deep Convolutional Neural Network Method

(2018) Chun Fang et al.   Journal of Bioinformatics and Computational Biology

Mutational analysis of gene function in the Anaplasmataceae: Challenges and perspectives

(2018) Adela S. Oliva Chávez et al.   Ticks and Tick-Borne Diseases

Predicting Protein-DNA Binding Residues by Weightedly Combining Sequence-Based Features and Boosting Multiple SVMs

(2017) Jun Hu et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Functional Analysis of Human Hub Proteins and Their Interactors Involved in the Intrinsic Disorder-Enriched Interactions

(2017) Gang Hu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

SMiLE-seq identifies binding motifs of single and dimeric transcription factors

(2017) Alina Isakova et al.   NATURE METHODS

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

An overview of multi-task learning

(2017) Yu Zhang et al.   National Science Review

Sequence-based prediction of protein-peptide binding sites using support vector machine

(2016) Ghazaleh Taherzadeh et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Molecular recognition features (MoRFs) in three domains of life

(2016) Jing Yan et al.   Molecular BioSystems

Protein–protein interaction sites prediction by ensembling SVM and sample-weighted random forests

(2016) Zhi-Sen Wei et al.   NEUROCOMPUTING

MoRFchibi SYSTEM: software tools for the identification of MoRFs in protein sequences

(2016) Nawar Malhis et al.   NUCLEIC ACIDS RESEARCH

Disordered nucleiome: Abundance of intrinsic disorder in the DNA- and RNA-binding proteins in 1121 species from Eukaryota, Bacteria and Archaea

(2016) Chen Wang et al.   PROTEOMICS

ATtRACT—a database of RNA-binding proteins and associated motifs

(2016) Girolamo Giudice et al.   Database-The Journal of Biological Databases and Curation

FastRNABindR: Fast and Accurate Prediction of Protein-RNA Interface Residues

(2016) Yasser EL-Manzalawy et al.   PLoS One

Computational identification of MoRFs in protein sequences

(2015) Nawar Malhis et al.   BIOINFORMATICS

A comprehensive comparative review of sequence-based predictors of DNA- and RNA-binding residues

(2015) Jing Yan et al.   BRIEFINGS IN BIOINFORMATICS

Progress and challenges in predicting protein interfaces

(2015) Reyhaneh Esmaielbeiki et al.   BRIEFINGS IN BIOINFORMATICS

In various protein complexes, disordered protomers have large per-residue surface areas and area of protein-, DNA- and RNA-binding interfaces

(2015) Zhonghua Wu et al.   FEBS LETTERS

Computational prediction of protein interfaces: A review of data driven methods

(2015) Li C. Xue et al.   FEBS LETTERS

Compartmentalization and Functionality of Nuclear Disorder: Intrinsic Disorder and Protein-Protein Interactions in Intra-Nuclear Compartments

(2015) Fanchi Meng et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

DNA-dependent formation of transcription factor pairs alters their binding specificity

(2015) Arttu Jolma et al.   NATURE

High-throughput prediction of RNA, DNA and protein binding regions mediated by intrinsic disorder

(2015) Zhenling Peng et al.   NUCLEIC ACIDS RESEARCH

A Large-Scale Assessment of Nucleic Acids Binding Site Prediction Programs

(2015) Zhichao Miao et al.   PLoS Computational Biology

Functional Advantages of Conserved Intrinsic Disorder in RNA-Binding Proteins

(2015) Mihaly Varadi et al.   PLoS One

DISOPRED3: precise disordered region predictions with annotated protein-binding activity

(2014) David T. Jones et al.   BIOINFORMATICS

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Exceptionally abundant exceptions: comprehensive characterization of intrinsic disorder in all domains of life

(2014) Zhenling Peng et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

RNABindRPlus: A Predictor that Combines Machine Learning and Sequence Homology-Based Methods to Improve the Reliability of Predicted RNA-Binding Residues in Proteins

(2014) Rasna R. Walia et al.   PLoS One

A creature with a hundred waggly tails: intrinsically disordered proteins in the ribosome

(2013) Zhenling Peng et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

mentha: a resource for browsing integrated protein-interaction networks

(2013) Alberto Calderone et al.   NATURE METHODS

Assessment of protein disorder region predictions in CASP10

(2013) Bohdan Monastyrskyy et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins

(2012) Fatemeh Miri Disfani et al.   BIOINFORMATICS

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

(2012) Limin Fu et al.   BIOINFORMATICS

Orderly order in protein intrinsic disorder distribution: disorder in 3500 proteomes from viruses and the three domains of life

(2012) Bin Xue et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Roles of intrinsic disorder in protein–nucleic acid interactions

(2011) H. Jane Dyson   Molecular BioSystems

BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features

(2010) Liangjiang Wang et al.   BMC Systems Biology

Hub Promiscuity in Protein-Protein Interaction Networks

(2010) Ashwini Patil et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

RBPDB: a database of RNA-binding specificities

(2010) K. B. Cook et al.   NUCLEIC ACIDS RESEARCH

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

3D-footprint: a database for the structural analysis of protein–DNA complexes

(2009) Bruno Contreras-Moreira   NUCLEIC ACIDS RESEARCH

Prediction of Protein Binding Regions in Disordered Proteins

(2009) Bálint Mészáros et al.   PLoS Computational Biology

Function and structure of inherently disordered proteins

(2008) A Keith Dunker et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY