P3DOCK: a protein–RNA docking webserver based on template-based and template-free docking

RMalign: an RNA structural alignment tool based on a novel scoring function RMscore

(2019) Jinfang Zheng et al.   BMC GENOMICS

Protein-RNA docking using ICM

(2018) Yelena A. Arnautova et al.   Journal of Chemical Theory and Computation

RNA–protein interaction detection in living cells

(2018) Muthukumar Ramanathan et al.   NATURE METHODS

Bioinformatics Tools and Benchmarks for Computational Docking and 3D Structure Prediction of RNA-Protein Complexes

(2018) Chandran Nithin et al.   Genes

Sampling Native-like Structures of RNA-Protein Complexes through Rosetta Folding and Docking

(2018) Kalli Kappel et al.   STRUCTURE

DSSR-enhanced visualization of nucleic acid structures in Jmol

(2017) Robert M. Hanson et al.   NUCLEIC ACIDS RESEARCH

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

A pair-conformation-dependent scoring function for evaluating 3D RNA-protein complex structures

(2017) Haotian Li et al.   PLoS One

Improved Accuracy in RNA–Protein Rigid Body Docking by Incorporating Force Field for Molecular Dynamics Simulation into the Scoring Function

(2016) Junichi Iwakiri et al.   Journal of Chemical Theory and Computation

irCLIP platform for efficient characterization of protein–RNA interactions

(2016) Brian J Zarnegar et al.   NATURE METHODS

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)

(2016) Eric L Van Nostrand et al.   NATURE METHODS

A non-redundant protein-RNA docking benchmark version 2.0

(2016) Chandran Nithin et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Template-Based Modeling of Protein-RNA Interactions

(2016) Jinfang Zheng et al.   PLoS Computational Biology

Protein-RNA networks revealed through covalent RNA marks

(2015) Christopher P Lapointe et al.   NATURE METHODS

NPDock: a web server for protein–nucleic acid docking

(2015) Irina Tuszynska et al.   NUCLEIC ACIDS RESEARCH

Protein-guided RNA dynamics during early ribosome assembly

(2014) Hajin Kim et al.   NATURE

Comprehensive analysis of RNA-protein interactions by high-throughput sequencing–RNA affinity profiling

(2014) Jacob M Tome et al.   NATURE METHODS

A census of human RNA-binding proteins

(2014) Stefanie Gerstberger et al.   NATURE REVIEWS GENETICS

A knowledge-based scoring function for protein-RNA interactions derived from a statistical mechanics-based iterative method

(2014) Sheng-You Huang et al.   NUCLEIC ACIDS RESEARCH

Protein-RNA Complexes and Efficient Automatic Docking: Expanding RosettaDock Possibilities

(2014) Adrien Guilhot-Gaudeffroy et al.   PLoS One

Evaluating template-based and template-free protein-protein complex structure prediction

(2013) T. Vreven et al.   BRIEFINGS IN BIOINFORMATICS

A novel protocol for three-dimensional structure prediction of RNA-protein complexes

(2013) Yangyu Huang et al.   Scientific Reports

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

(2012) Limin Fu et al.   BIOINFORMATICS

A nonredundant structure dataset for benchmarking protein-RNA computational docking

(2012) Sheng-You Huang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Templates are available to model nearly all complexes of structurally characterized proteins

(2012) P. J. Kundrotas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking

(2011) Irina Tuszynska et al.   BMC BIOINFORMATICS

A coarse-grained force field for Protein–RNA docking

(2011) Piotr Setny et al.   NUCLEIC ACIDS RESEARCH

A new residue-nucleotide propensity potential with structural information considered for discriminating protein-RNA docking decoys

(2011) Chun Hua Li et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Quantifying the relationship between sequence and three-dimensional structure conservation in RNA

(2010) Emidio Capriotti et al.   BMC BIOINFORMATICS

Genome-wide Identification of Polycomb-Associated RNAs by RIP-seq

(2010) Jing Zhao et al.   MOLECULAR CELL

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution

(2010) Julian König et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

MDockPP: A hierarchical approach for protein-protein docking and its application to CAPRI rounds 15-19

(2010) Sheng-You Huang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Binding of the Bacteriophage P22 N-Peptide to the boxB RNA Motif Studied by Molecular Dynamics Simulations

(2009) Ranjit P. Bahadur et al.   BIOPHYSICAL JOURNAL

Structure is three to ten times more conserved than sequence-A study of structural response in protein cores

(2009) Kristoffer Illergård et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS