Computational prediction of RNA-binding proteins and binding sites
J Si, J Cui, J Cheng, R Wu - International journal of molecular sciences, 2015 - mdpi.com
Proteins and RNA interaction have vital roles in many cellular processes such as protein
synthesis, sequence encoding, RNA transfer, and gene regulation at the transcriptional and …
synthesis, sequence encoding, RNA transfer, and gene regulation at the transcriptional and …
[HTML][HTML] Structural studies of RNA-protein complexes: A hybrid approach involving hydrodynamics, scattering, and computational methods
The diverse functional cellular roles played by ribonucleic acids (RNA) have emphasized
the need to develop rapid and accurate methodologies to elucidate the relationship between …
the need to develop rapid and accurate methodologies to elucidate the relationship between …
Assessing the performance of MM/PBSA and MM/GBSA methods. 8. Predicting binding free energies and poses of protein–RNA complexes
Molecular docking provides a computationally efficient way to predict the atomic structural
details of protein–RNA interactions (PRI), but accurate prediction of the three-dimensional …
details of protein–RNA interactions (PRI), but accurate prediction of the three-dimensional …
Investigating the mechanism of recognition and structural dynamics of nucleoprotein-RNA complex from Peste des petits ruminants virus via Gaussian accelerated …
The nucleocapsid (N) protein from Peste des petits ruminants virus enwraps the nascent
genomic RNA primarily to protect it from cellular enzymatic degradation. Here, we have …
genomic RNA primarily to protect it from cellular enzymatic degradation. Here, we have …
Sampling native-like structures of RNA-protein complexes through Rosetta folding and docking
RNA-protein complexes underlie numerous cellular processes including translation,
splicing, and posttranscriptional regulation of gene expression. The structures of these …
splicing, and posttranscriptional regulation of gene expression. The structures of these …
In silico aptamer docking studies: from a retrospective validation to a prospective case study'tim3 aptamers binding
Complementing Systematic Evolution of Ligands by EXponential Enrichment (SELEX)
technologies with in silico prediction of aptamer binders has attracted a lot of interest in the …
technologies with in silico prediction of aptamer binders has attracted a lot of interest in the …
[HTML][HTML] Computational modeling of RNA 3D structures and interactions
WK Dawson, JM Bujnicki - Current opinion in structural biology, 2016 - Elsevier
Highlights•We discuss the two main schools of thought in RNA 3D modeling: fundamental
principles ('Greek science') versus knowledge-based ('Babylonian science').•We discuss the …
principles ('Greek science') versus knowledge-based ('Babylonian science').•We discuss the …
Template-based modeling of protein-RNA interactions
Protein-RNA complexes formed by specific recognition between RNA and RNA-binding
proteins play an important role in biological processes. More than a thousand of such …
proteins play an important role in biological processes. More than a thousand of such …
E2edna: Simulation protocol for dna aptamers with ligands
We present E2EDNA, a simulation protocol and accompanying code for the molecular
biophysics and materials science communities. This protocol is both easy to use and …
biophysics and materials science communities. This protocol is both easy to use and …
Frontiers and Challenges of Computing ncRNAs Biogenesis, Function and Modulation
Non-coding RNAs (ncRNAs), generated from nonprotein coding DNA sequences, constitute
98–99% of the human genome. Non-coding RNAs encompass diverse functional classes …
98–99% of the human genome. Non-coding RNAs encompass diverse functional classes …