ArticlePLoS computational biology2016
Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 26 citations in OpenAlex.
- RmsdXNA: RMSD prediction of nucleic acid-ligand docking poses using machine-learning method.Briefings in bioinformatics · 2024Article
- HIPPO: HIstogram-based Pseudo-POtential for scoring protein-ssRNA fragment-based docking poses.BMC bioinformatics · 2024Article
- Construction of Histone-Protein Complex Structures by Peptide Growing.International journal of molecular sciences · 2023Article
- Conformational variability in proteins bound to single-stranded DNA: A new benchmark for new docking perspectives.Proteins · 2022Article
- A CRISPR-Cas12a integrated SERS nanoplatform with chimeric DNA/RNA hairpin guide for ultrasensitive nucleic acid detection.Theranostics · 2022Article
- An overview of structural approaches to study therapeutic RNAs.Frontiers in molecular biosciences · 2022Review
- Structure, stability and specificity of the binding of ssDNA and ssRNA with proteins.PLoS computational biology · 2019Article
- Sampling Native-like Structures of RNA-Protein Complexes through Rosetta Folding and Docking.Structure (London, England : 1993) · 2019Article
- Protein-RNA interactions: structural biology and computational modeling techniques.Biophysical reviews · 2016Review
- Recent Advances in Developing Small Molecules Targeting Nucleic Acid.International journal of molecular sciences · 2016Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein-RNA docking is hampered by the high flexibility of RNA, and particularly single-stranded RNA (ssRNA). Yet, ssRNA regions typically carry the specificity of protein recognition. The lack of methodology for modeling such regions limits the accuracy of current protein-RNA docking methods. We developed a fragment-based approach to model protein-bound ssRNA, based on the structure of the protein and the sequence of the RNA, without any prior knowledge of the RNA binding site or the RNA structure. The conformational diversity of each fragment is sampled by an exhaustive RNA fragment library that was created from all the existing experimental structures of protein-ssRNA complexes. A systematic and detailed analysis of fragment-based ssRNA docking was performed which constitutes a proof-of-principle for the fragment-based approach. The method was tested on two 8-homo-nucleotide ssRNA-protein complexes and was able to identify the binding site on the protein within 10 Å. Moreover, a structure of each bound ssRNA could be generated in close agreement with the crystal structure with a mean deviation of ~1.5 Å except for a terminal nucleotide. This is the first time a bound ssRNA could be modeled from sequence with high precision.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.