Research graph
References from Transcription reshapes RNA hairpin folding pathways revealed by all-atom molecular dynamics simulations. Local targets link to admitted publications; unresolved targets remain external evidence.
Accurate structure prediction of biomolecular interactions with AlphaFold 3
10.1038/s41586-024-07487-w · 2024 · External reference
RNA dynamics: it is about time
10.1016/j.sbi.2008.04.004 · 2008 · External reference
Co-transcriptional gene regulation in eukaryotes and prokaryotes
10.1038/s41580-024-00706-2 · 2024 · External reference
Cotranscriptional folding of RNA pseudoknots with different rates
10.1016/j.cplett.2021.138946 · 2021 · External reference
Transcriptional pausing at the translation start site operates as a critical checkpoint for riboswitch regulation
10.1038/ncomms13892 · 2017 · External reference
Types and concentrations of metal ions affect local structure and dynamics of RNA
10.1103/physreve.94.040401 · 2016 · External reference
Transcription Regulation Through Nascent RNA Folding
10.1016/j.jmb.2021.166975 · 2021 · External reference
Direct observation of cotranscriptional folding in an adenine riboswitch
10.1126/science.1225722 · 2012 · External reference
Single-molecule FRET studies on the cotranscriptional folding of a thiamine pyrophosphate riboswitch
10.1073/pnas.1712983115 · 2018 · External reference
Co-transcriptional folding of the glmS ribozyme enables a rapid response to metabolite
10.1093/nar/gkad1120 · 2024 · External reference
Cotranscriptional folding of a riboswitch at nucleotide resolution
10.1038/nsmb.3316 · 2016 · External reference
In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding
2017 · External reference
Genome-wide probing of eukaryotic nascent RNA structure elucidates cotranscriptional folding and its antimutagenic effect
10.1038/s41467-023-41550-w · 2023 · External reference
Observation of coordinated RNA folding events by systematic cotranscriptional RNA structure probing
10.1038/s41467-023-43395-9 · 2023 · External reference
Differences between cotranscriptional and free riboswitch folding
10.1093/nar/gkt1213 · 2014 · External reference
Effect of pausing on the cotranscriptional folding kinetics of RNAs
10.1016/j.ijbiomac.2022.09.115 · 2022 · External reference
Landscape Zooming toward the Prediction of RNA Cotranscriptional Folding
10.1021/acs.jctc.1c01233 · 2022 · External reference
Kinetic pathway of HIV-1 TAR cotranscriptional folding
10.1093/nar/gkae362 · 2024 · External reference
How does RNA fold dynamically?
10.1016/j.jmb.2022.167665 · 2022 · External reference
Co-Transcriptional Folding and Regulation Mechanisms of Riboswitches
10.3390/molecules22071169 · 2017 · External reference
Regulatory effects of cotranscriptional RNA structure formation and transitions
10.1002/wrna.1350 · 2016 · External reference
Molecular dynamics study of ways of RNA base-pair formation
10.1103/physreve.102.032403 · 2020 · External reference
Molecular Dynamics Simulation of a RNA Aptasensor
10.1021/acs.jpcb.6b12544 · 2017 · External reference
The thermodynamics and kinetics of a nucleotide base pair
10.1063/1.4944067 · 2016 · External reference
A Two-Way Street: Regulatory Interplay between RNA Polymerase and Nascent RNA Structure
10.1016/j.tibs.2015.12.009 · 2016 · External reference
The Amber biomolecular simulation programs
10.1002/jcc.20290 · 2005 · External reference
Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles
10.1021/ct200162x · 2011 · External reference
Systematic Parameterization of Monovalent Ions Employing the Nonbonded Model
10.1021/ct500918t · 2015 · External reference
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
10.1016/0021-9991(77)90098-5 · 1977 · External reference
Molecular dynamics with coupling to an external bath
10.1063/1.448118 · 1984 · External reference
Particle mesh Ewald: An N⋅ log (N) method for Ewald sums in large systems
10.1063/1.464397 · 1993 · External reference
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald
10.1021/ct400314y · 2013 · External reference
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
10.1021/ct400341p · 2013 · External reference
Pymol: An open-source molecular graphics tool
2002 · External reference
Protein folding by zipping and assembly
10.1073/pnas.0703700104 · 2007 · External reference
Role of cotranslational folding for β-sheet-enriched proteins: A perspective from molecular dynamics simulations
10.1103/physreve.105.024402 · 2022 · External reference
Pathway regulation mechanism revealed by cotranslational folding of villin headpiece subdomain HP35
10.1103/physreve.101.052403 · 2020 · External reference
Pathway regulation mechanism by cotranslational protein folding
10.1038/s42004-025-01636-6 · 2025 · External reference
Data-driven detection of critical points of phase transitions in complex systems
2023 · External reference
Trigger factor accelerates nascent chain compaction and folding
10.1073/pnas.2422678122 · 2025 · External reference
Energy landscapes, folding mechanisms, and kinetics of RNA tetraloop hairpins
10.1021/ja5100756 · 2014 · External reference
Bridging the gap between in vitro and in vivo RNA folding
10.1017/s003358351600007x · 2016 · External reference
Using the generalized Born surface area model to fold proteins yields more effective sampling while qualitatively preserving the folding landscape
10.1103/physreve.101.062417 · 2020 · External reference
Advances in RNA molecular dynamics: a simulator’s guide to RNA force fields
10.1002/wrna.1396 · 2017 · External reference
RNA force field with accuracy comparable to state-of-the-art protein force fields
2018 · External reference
Development of Force Field Parameters for the Simulation of Single- and Double-Stranded DNA Molecules and DNA-Protein Complexes
10.1021/acs.jpcb.1c10971 · 2022 · External reference
Revised AMBER Parameters for Bioorganic Phosphates
10.1021/ct300613v · 2012 · External reference
Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field
10.1021/acs.jctc.2c00200 · 2022 · External reference
