A protein–RNA docking benchmark (I): Nonredundant cases

No abstract is available for this paper.

• Publication year

  2012

• Venue

  Proteins: Structure, Function, and Bioinformatics

• Publication date

  2012-07-01

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.1002/prot.24083PMID 22488669
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• The role of RNA sequence and structure in RNA--protein interactions.

  2011cited by this paper
• The targets of CAPRI Rounds 13–19

  2010cited by this paper
• Optimal protein‐RNA area, OPRA: A propensity‐based method to identify RNA‐binding sites on proteins

  2010cited by this paper
• Protein–protein interaction and quaternary structure

  2008cited by this paper
• Recent progress and future directions in protein-protein docking.

  2008cited by this paper
• Dissecting protein–RNA recognition sites

  2008cited by this paper
• Protein–protein docking benchmark version 3.0

  2008cited by this paper
• Relating Macromolecular Function and Association: The Structural Basis of Protein–DNA and RNA Recognition

  2008cited by this paper
• A protein–DNA docking benchmark

  2008cited by this paper
• Structure of the ribosomal protein L1-mRNA complex at 2.1 A resolution: common features of crystal packing of L1-RNA complexes.

  2006cited by this paper
• RNA recognition by the Vts1p SAM domain

  2006cited by this paper
• Crystallization of RNA and RNA-protein complexes.

  2004cited by this paper
• Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA recognition through a combination of rigid docking and induced fit

  2003cited by this paper
• NMR structure of the 3' stem-loop from human U4 snRNA.

  2002cited by this paper
• Structural genomics of RNA

  2000cited by this paper
• Crystal structure of the spliceosomal 15.5kD protein bound to a U4 snRNA fragment.

  2000cited by this paper
• DaliLite workbench for protein structure comparison

  2000cited by this paper
• A mutant form of the ribosomal protein L1 reveals conformational flexibility

  1997cited by this paper
• The interpretation of protein structures: estimation of static accessibility.

  1971cited by this paper
• Electronic Reprint Biological Crystallography the Protein Data Bank Biological Crystallography the Protein Data Bank

  year unknowncited by this paper

• Precision in Predicting Protein-Nucleic Acid Complexes: Establishing a Benchmark Data Set and Comparative Metrics

  2025cites this paper
• Conformational switches in human RNA binding proteins involved in neurodegeneration.

  2025cites this paper
• Protein‐RNA Docking Benchmark v3.0 Integrated With Binding Affinity

  2025cites this paper
• Dynamics of Protein-RNA Interfaces Using All-Atom Molecular Dynamics Simulations.

  2024cites this paper
• Advances and Challenges in Scoring Functions for RNA–Protein Complex Structure Prediction

  2024cites this paper
• The dynamics of protein-RNA interfaces using all-atom molecular dynamics simulations

  2024cites this paper
• Efficient mapping of RNA‐binding residues in RNA‐binding proteins using local sequence features of binding site residues in protein‐RNA complexes

  2023cites this paper
• Challenges in structural modeling of RNA-protein interactions.

  2023cites this paper
• Advanced computational tools for quantitative analysis of protein–nucleic acid interfaces

  2022cites this paper
• Internal Normal Mode Analysis applied to RNA flexibility and conformational changes

  2022cites this paper
• Guanidinium-amino acid hydrogen-bonding interactions in protein crystal structures: implications for guanidinium-induced protein denaturation.

  2022cites this paper
• pyDockDNA: A new web server for energy-based protein-DNA docking and scoring

  2022influential citation
• MCSS-Based Predictions of Binding Mode and Selectivity of Nucleotide Ligands.

  2021cites this paper
• Protein-ensemble-RNA docking by efficient consideration of protein flexibility through homology models

  2019cites this paper
• PredPRBA: Prediction of Protein-RNA Binding Affinity Using Gradient Boosted Regression Trees

  2019cites this paper
• A structure-based model for the prediction of protein–RNA binding affinity

  2019cites this paper
• Protein-assisted RNA fragment docking (RnaX) for modeling RNA–protein interactions using ModelX

  2019cites this paper
• MCSS-based Docking and Improved Scoring of Protein-Nucleotide Complexes: I. A step forward to the Fragment-Based Design of Oligonucleotides

  2019cites this paper
• Assessing the performance of MM/PBSA and MM/GBSA methods. 8. Predicting binding free energies and poses of protein–RNA complexes

  2018cites this paper
• An account of solvent accessibility in protein-RNA recognition

  2018cites this paper
• Protein-RNA Docking Using ICM.

  2018cites this paper
• Bioinformatics Tools and Benchmarks for Computational Docking and 3D Structure Prediction of RNA-Protein Complexes

  2018cites this paper
• RRDB: a comprehensive and non‐redundant benchmark for RNA‐RNA docking and scoring

  2018cites this paper
• A non‐redundant protein–RNA docking benchmark version 2.0

  2017cites this paper
• Crystal structure of a DNA aptamer bound to PvLDH elucidates novel single-stranded DNA structural elements for folding and recognition

  2016cites this paper
• Template-Based Modeling of Protein-RNA Interactions

  2016cites this paper
• A structural perspective of RNA recognition by intrinsically disordered proteins

  2016cites this paper
• Analysis of Interactions and Dissection of Interfaces Involved in RNA-Protein Recognition.

  2016cites this paper
• Prospective observational study protocol to investigate long-term adverse effects of methylphenidate in children and adolescents with ADHD: the Attention Deficit Hyperactivity Disorder Drugs Use Chronic Effects (ADDUCE) study

  2016cites this paper
• Knowledge-based approaches for understanding structure-dynamics-function relationship in proteins

  2016influential citation
• Improved Accuracy in RNA-Protein Rigid Body Docking by Incorporating Force Field for Molecular Dynamics Simulation into the Scoring Function.

  2016cites this paper
• Bio/chemoinformatics in India: an outlook

  2015cites this paper
• Prediction of nucleic acid binding probability in proteins: a neighboring residue network based score

  2015cites this paper
• On the use of knowledge-based potentials for the evaluation of models of protein-protein, protein-DNA, and protein-RNA interactions.

  2014cites this paper
• Bio/chemoinformatics in India: an

  2014cites this paper
• An analysis of conformational changes upon RNA-protein binding

  2014cites this paper
• Hydration of protein–RNA recognition sites

  2014cites this paper
• Sequence-based prediction of RNA-protein interactions

  2014influential citation
• A knowledge-based scoring function for protein-RNA interactions derived from a statistical mechanics-based iterative method

  2014cites this paper
• Protein-RNA Complexes and Efficient Automatic Docking: Expanding RosettaDock Possibilities

  2014influential citation
• The dataset for protein–RNA binding affinity

  2013cites this paper
• Optimizing Scoring Function of Protein-Nucleic Acid Interactions with Both Affinity and Specificity

  2013cites this paper
• Preorientation of protein and RNA just before contacting

  2013cites this paper
• PRince: a web server for structural and physicochemical analysis of Protein-RNA interface

  2012cites this paper