Template-Based Modeling of Protein-RNA Interactions

Affinity regression predicts the recognition code of nucleic acid–binding proteins

(2015) Raphael Pelossof et al.   NATURE BIOTECHNOLOGY

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

RPI-Pred: predicting ncRNA-protein interaction using sequence and structural information

(2015) V. Suresh et al.   NUCLEIC ACIDS RESEARCH

Protein models docking benchmark 2

(2015) Ivan Anishchenko et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein-Protein Docking: From Interaction to Interactome

(2014) Ilya A. Vakser   BIOPHYSICAL JOURNAL

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

LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs

(2014) Lina Ma et al.   NUCLEIC ACIDS RESEARCH

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

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

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

Computational prediction of associations between long non-coding RNAs and proteins

(2013) Qiongshi Lu et al.   BMC GENOMICS

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

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

Low-resolution structural modeling of protein interactome

(2013) Ilya A Vakser   CURRENT OPINION IN STRUCTURAL BIOLOGY

Rise of the RNA Machines: Exploring the Structure of Long Non-Coding RNAs

(2013) Irina V. Novikova et al.   JOURNAL OF MOLECULAR BIOLOGY

Computational modeling of protein–RNA complex structures

(2013) Irina Tuszynska et al.   METHODS

RNA global alignment in the joint sequence–structure space using elastic shape analysis

(2013) Jose Laborde et al.   NUCLEIC ACIDS RESEARCH

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Protein-protein alternative binding modes do not overlap

(2013) Petras J. Kundrotas et al.   PROTEIN SCIENCE

Structural templates for modeling homodimers

(2013) Petras J. Kundrotas et al.   PROTEIN SCIENCE

Global and local structural similarity in protein-protein complexes: Implications for template-based docking

(2013) Petras J. Kundrotas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Docking, scoring, and affinity prediction in CAPRI

(2013) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND 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

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins

(2012) Alfredo Castello et al.   CELL

De novo prediction of RNA–protein interactions from sequence information

(2012) Ying Wang et al.   Molecular BioSystems

The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts

(2012) Alexander G. Baltz et al.   MOLECULAR CELL

Protein Docking by the Interface Structure Similarity: How Much Structure Is Needed?

(2012) Rohita Sinha et al.   PLoS One

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

Predicting RNA-Protein Interactions Using Only Sequence Information

(2011) Usha K Muppirala et al.   BMC BIOINFORMATICS

Predicting protein associations with long noncoding RNAs

(2011) Matteo Bellucci et al.   NATURE METHODS

A coarse-grained force field for Protein–RNA docking

(2011) Piotr Setny et al.   NUCLEIC ACIDS RESEARCH

Dissecting the protein–RNA interface: the role of protein surface shapes and RNA secondary structures in protein–RNA recognition

(2011) Junichi Iwakiri 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

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets

(2010) H. Zhao et al.   NUCLEIC ACIDS RESEARCH

Docking by structural similarity at protein-protein interfaces

(2010) Rohita Sinha et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

RNA Folding: Conformational Statistics, Folding Kinetics, and Ion Electrostatics

(2008) Shi-Jie Chen   Annual Review of Biophysics

RNA structure alignment by a unit-vector approach

(2008) E. Capriotti et al.   BIOINFORMATICS

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

(2008) Donny D. Licatalosi et al.   NATURE

Dissecting protein–RNA recognition sites

(2008) Ranjit Prasad Bahadur et al.   NUCLEIC ACIDS RESEARCH

The size of the intermolecular energy funnel in protein-protein interactions

(2008) Jagtar Hunjan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS