Research graph
References from 3D structure and stability prediction of DNA with multi-way junctions in ionic solutions. Local targets link to admitted publications; unresolved targets remain external evidence.
A brief review on DNA storage, compression, and digitalization
10.1016/j.nancom.2021.100391 · 2022 · External reference
Biologic synthesis of deoxyribonucleic acid: An isolated enzyme catalyzes synthesis of this nucleic acid in response to directions from pre-existing DNA
10.1126/science.131.3412.1503 · 1960 · External reference
DNA supercoiling: another level for regulating gene expression
10.1016/0092-8674(81)90085-4 · 1981 · External reference
Non-B DNA: a major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome
10.1093/nar/gkaa1269 · 2021 · External reference
DNA-based construction at the nanoscale: emerging trends and applications
10.1088/1361-6528/aaa120 · 2018 · External reference
Engineering three-dimensional genome folding
10.1038/s41588-021-00860-9 · 2021 · External reference
Organization and function of the 3D genome
10.1038/nrg.2016.112 · 2016 · External reference
Determinants of enhancer and promoter activities of regulatory elements
10.1038/s41576-019-0173-8 · 2020 · External reference
Creating complex molecular topologies by configuring DNA four-way junctions
10.1038/nchem.2564 · 2016 · External reference
Transmission of dynamic supercoiling in linear and multi-way branched DNAs and its regulation revealed by a fluorescent G-quadruplex torsion sensor
10.1093/nar/gky534 · 2018 · External reference
The RCSB protein data bank: integrative view of protein, gene and 3D structural information
2016 · External reference
Protein Data Bank (PDB): the single global macromolecular structure archive
10.1007/978-1-4939-7000-1_26 · 2017 · External reference
Ab initio predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions
2022 · External reference
Computational Modeling of DNA 3D Structures: From Dynamics and Mechanics to Folding
10.3390/molecules28124833 · 2023 · External reference
GenBank
10.1093/nar/gks1195 · 2012 · External reference
GenBank
10.1093/nar/gkx1094 · 2018 · External reference
Structure and Dynamics of dsDNA in Cell-like Environments
10.3390/e24111587 · 2022 · External reference
Accurate structure prediction of biomolecular interactions with AlphaFold 3
10.1038/s41586-024-07487-w · 2024 · External reference
Highly accurate protein structure prediction with AlphaFold
10.1038/s41586-021-03819-2 · 2021 · External reference
trRosettaRNA: automated prediction of RNA 3D structure with transformer network
10.1038/s41467-023-42528-4 · 2023 · External reference
Integrating end-to-end learning with deep geometrical potentials for ab initio RNA structure prediction
10.1038/s41467-023-41303-9 · 2023 · External reference
Accurate RNA 3D structure prediction using a language model-based deep learning approach
2024 · External reference
Predicting DNA structure using a deep learning method
10.1038/s41467-024-45191-5 · 2024 · External reference
Structure Prediction of Large RNAs with AlphaFold3 Highlights its Capabilities and Limitations
10.1016/j.jmb.2024.168816 · 2024 · External reference
3dRNA: 3D Structure Prediction from Linear to Circular RNAs
10.1016/j.jmb.2022.167452 · 2022 · External reference
Using 3dRNA/DNA for RNA and DNA 3D Structure Prediction and Evaluation
10.1002/cpz1.770 · 2023 · External reference
NNDB: An Expanded Database of Nearest Neighbor Parameters for Predicting Stability of Nucleic Acid Secondary Structures
10.1016/j.jmb.2024.168549 · 2024 · External reference
Increasing the Accuracy and Robustness of the CHARMM General Force Field with an Expanded Training Set
10.1021/acs.jctc.5c00046 · 2025 · External reference
CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields
10.1002/jcc.21367 · 2010 · External reference
Multivalent Cations Reverse the Twist-Stretch Coupling of RNA
10.1103/physrevlett.128.108103 · 2022 · External reference
The origin of different bending stiffness between double-stranded RNA and DNA revealed by magnetic tweezers and simulations
10.1093/nar/gkae063 · 2024 · External reference
Lipid21: Complex Lipid Membrane Simulations with AMBER
10.1021/acs.jctc.1c01217 · 2022 · External reference
Multiscale simulation of DNA
10.1016/j.sbi.2015.11.011 · 2016 · External reference
Coarse-grained modeling of DNA–RNA hybrids
10.1063/5.0199558 · 2024 · External reference
A coarse-grained model for DNA origami
10.1093/nar/gkx1262 · 2018 · External reference
Martini 3: a general purpose force field for coarse-grained molecular dynamics
10.1038/s41592-021-01098-3 · 2021 · External reference
Accurate Sequence-Dependent Coarse-Grained Model for Conformational and Elastic Properties of Double-Stranded DNA
10.1021/acs.jctc.2c00138 · 2022 · External reference
Holliday junction thermodynamics and structure: comparisons of coarse-grained simulations and experiments
10.1016/j.bpj.2015.11.992 · 2016 · External reference
OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures
10.1093/nar/gkab324 · 2021 · External reference
A coarse-grain three-site-per-nucleotide model for DNA with explicit ions
10.1063/1.3652956 · 2011 · External reference
Sequence-Dependent Three Interaction Site Model for Single- and Double-Stranded DNA
10.1021/acs.jctc.8b00091 · 2018 · External reference
Optimization of a Nucleic Acids united-RESidue 2-Point model (NARES-2P) with a maximum-likelihood approach
10.1063/1.4932082 · 2015 · External reference
Coarse-Grained HiRE-RNA Model for ab Initio RNA Folding beyond Simple Molecules, Including Noncanonical and Multiple Base Pairings
10.1021/acs.jctc.5b00200 · 2015 · External reference
Stretching single-stranded DNA: interplay of electrostatic, base-pairing, and base-pair stacking interactions
10.1016/s0006-3495(01)75770-0 · 2001 · External reference
Twisting DNA by salt
10.1093/nar/gkac445 · 2022 · External reference
Understanding nucleic acid-ion interactions
10.1146/annurev-biochem-060409-092720 · 2014 · External reference
Differential stability of DNA based on salt concentration
10.1007/s00249-016-1132-3 · 2017 · External reference
Electrostatic free energy landscapes for nucleic acid helix assembly
10.1093/nar/gkl810 · 2006 · External reference
An experimentally-informed coarse-grained 3-Site-Per-Nucleotide model of DNA: structure, thermodynamics, and dynamics of hybridization
10.1063/1.4822042 · 2013 · External reference
A coarse grain model for DNA
10.1063/1.2431804 · 2007 · External reference
Coarse-grained modeling of DNA curvature
10.1063/1.4897649 · 2014 · External reference
Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model
10.1063/1.3552946 · 2011 · External reference
Understanding DNA interactions in crowded environments with a coarse-grained model
10.1093/nar/gkaa854 · 2020 · External reference
Generalized Manning Condensation Model Captures the RNA Ion Atmosphere
10.1103/physrevlett.114.258105 · 2015 · External reference
Theory and simulations for RNA folding in mixtures of monovalent and divalent cations
10.1073/pnas.1911632116 · 2019 · External reference
Predicting 3D Structure, Flexibility, and Stability of RNA Hairpins in Monovalent and Divalent Ion Solutions
10.1016/j.bpj.2015.11.006 · 2015 · External reference
Predicting 3D structures and stabilities for complex RNA pseudoknots in ion solutions
10.1016/j.bpj.2023.03.017 · 2023 · External reference
The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides
10.1017/s0033583500002031 · 1978 · External reference
Nucleic acid helix stability: effects of salt concentration, cation valence and size, and chain length
10.1529/biophysj.105.070904 · 2006 · External reference
A coarse-grained model with implicit salt for RNAs: predicting 3D structure, stability and salt effect
10.1063/1.4894752 · 2014 · External reference
Exchange Monte Carlo method and application to spin glass simulations
10.1143/jpsj.65.1604 · 1996 · External reference
Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations
10.1016/j.jmgm.2003.12.009 · 2004 · External reference
On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: application to protein structure prediction
10.1063/1.1472510 · 2002 · External reference
SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction
10.1093/nar/gkv1479 · 2016 · External reference
QRNAS: software tool for refinement of nucleic acid structures
10.1186/s12900-019-0103-1 · 2019 · External reference
Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations
10.1021/ct0502864 · 2007 · External reference
Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson− Crick base pairs
10.1021/bi9809425 · 1998 · External reference
10.1145/336154.336189
10.1145/336154.336189 · External reference
Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions
2018 · External reference
Automated and fast building of three-dimensional RNA structures
10.1038/srep00734 · 2012 · External reference
IsRNA: An Iterative Simulated Reference State Approach to Modeling Correlated Interactions in RNA Folding
10.1021/acs.jctc.7b01228 · 2018 · External reference
RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning
10.1038/s41467-019-13395-9 · 2019 · External reference
RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction
10.1261/rna.031054.111 · 2012 · External reference
Global structure of a DNA three-way junction by solution NMR: towards prediction of 3H fold
10.1093/nar/gkh645 · 2004 · External reference
A structural explanation for the antithrombotic activity of ARC1172, a DNA aptamer that binds von Willebrand factor domain A1
10.1016/j.str.2009.09.011 · 2009 · External reference
Solution Structure of a Lanthanide-binding DNA Aptamer Determined Using High Quality pseudocontact shift restraints
2022 · External reference
3dRNA/DNA: 3D Structure Prediction from RNA to DNA
10.1016/j.jmb.2024.168742 · 2024 · External reference
Effect of GCAA stabilizing loops on three- and four-way intramolecular junctions
10.1039/c7cp08329g · 2018 · External reference
Opposite Effects of High-Valent Cations on the Elasticities of DNA and RNA Duplexes Revealed by Magnetic Tweezers
10.1103/physrevlett.124.058101 · 2020 · External reference
Counterintuitive DNA destabilization by monovalent salt at high concentrations due to overcharging
10.1038/s41467-024-55404-6 · 2025 · External reference
Unusual similarity of DNA solvation dynamics in high-salinity crowding with divalent cations of varying concentrations
10.1039/d3cp02606j · 2023 · External reference
Mfold web server for nucleic acid folding and hybridization prediction
10.1093/nar/gkg595 · 2003 · External reference
Non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis
10.1080/07391102.2006.10507108 · 2006 · External reference
Conformational specificity of non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis
10.1007/s10822-006-9083-x · 2006 · External reference
Structure and mechanism of formation of the H-y5 isomer of an intramolecular DNA triple helix
10.1038/12313 · 1999 · External reference
Solution structure of an intramolecular DNA triplex containing an N7-glycosylated guanine which mimics a protonated cytosine
10.1021/bi962438a · 1997 · External reference
G-quadruplex structures are stable and detectable in human genomic DNA
10.1038/ncomms2792 · 2013 · External reference
DNA G-quadruplex structures mold the DNA methylome
10.1038/s41594-018-0131-8 · 2018 · External reference
rsRNASP: A residue-separation-based statistical potential for RNA 3D structure evaluation
10.1016/j.bpj.2021.11.016 · 2022 · External reference
DNA melting in the presence of molecular crowders
10.1039/c7cp03624h · 2017 · External reference
Force-induced unzipping of DNA in the presence of solvent molecules
10.1016/j.bpc.2024.107175 · 2024 · External reference
VARNA: Interactive drawing and editing of the RNA secondary structure
10.1093/bioinformatics/btp250 · 2009 · External reference
Pymol: An open-source molecular graphics tool
2002 · External reference
