Coarse-grained modeling of RNA 3D structure

scientific article published in July 2016

Coarse-grained modeling of RNA 3D structure is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1016/J.YMETH.2016.04.026
P3181OpenCitations bibliographic resource ID3393654
P698PubMed publication ID27125734

P50authorJanusz BujnickiQ11720088
Wayne K. DawsonQ56090089
Maciej MaciejczykQ62027544
P2093author name stringElzbieta J Jankowska
P2860cites workEquation of State Calculations by Fast Computing MachinesQ5384234
A probabilistic model of RNA conformational spaceQ21145357
Potentials of mean force for protein structure prediction vindicated, formalized and generalizedQ21562146
Multicanonical ensemble: A new approach to simulate first-order phase transitionsQ21698968
Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knotsQ24530528
Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulationsQ24618750
Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filtersQ24647503
iFoldRNA: three-dimensional RNA structure prediction and foldingQ24658133
Automated de novo prediction of native-like RNA tertiary structuresQ24673712
Optimization by Simulated AnnealingQ25939004
Computational modeling of RNA 3D structures and interactionsQ26774511
Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulationsQ26822885
Design and application of implicit solvent models in biomolecular simulationsQ26866327
Molecular recognition and function of riboswitchesQ27000757
A decade of riboswitchesQ27000960
Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)Q27332083
Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10Q27680838
All-atom empirical potential for molecular modeling and dynamics studies of proteinsQ27860468
The Amber biomolecular simulation programsQ27860745
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structureQ27860806
Hierarchy and dynamics of RNA foldingQ28244994
Exploring the folding free energy landscape of a β-hairpin miniprotein, chignolin, using multiscale free energy landscape calculation methodQ84292937
Coarse-grained model for predicting RNA folding thermodynamicsQ86487529
RNA pseudo-knots simulated with a one-bead coarse-grained modelQ87489810
A nucleotide-level coarse-grained model of RNAQ88127110
Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic LiquidsQ99192955
The folding of single domain proteins--have we reached a consensus?Q37818728
Accounting for electronic polarization in non-polarizable force fieldsQ37826630
Computational approaches to RNA structure prediction, analysis, and designQ37868135
Cations in charge: magnesium ions in RNA folding and catalysisQ38010818
Systematic methods for structurally consistent coarse-grained modelsQ38049271
Coarse-graining methods for computational biologyQ38085672
Perspective on the Martini model.Q38109488
How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialistsQ38112952
Perspective: Coarse-grained models for biomolecular systemsQ38136697
Exploring the electrostatic energy landscape for tetraloop-receptor docking.Q38280278
Simple, yet powerful methodologies for conformational sampling of proteins.Q38346856
TectoRNA: modular assembly units for the construction of RNA nano-objectsQ38659215
Computational prediction of riboswitch tertiary structures including pseudoknots by RAGTOP: a hierarchical graph sampling approachQ39034408
Improved Parameters for the Martini Coarse-Grained Protein Force Field.Q40295743
Modeling DNA loops using the theory of elasticityQ40335218
Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structuresQ40775428
Computational methods toward accurate RNA structure prediction using coarse-grained and all-atom modelsQ41333974
Modeling complex RNA tertiary folds with RosettaQ41333985
Coarse-grained model for simulation of RNA three-dimensional structures.Q41688309
Predicting the three-dimensional folding of transfer RNA with a computer modeling protocolQ41768175
Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structureQ41994677
Encoding folding paths of RNA switchesQ42021639
DNA hybridization kinetics: zippering, internal displacement and sequence dependenceQ42235592
Structure and mechanical properties of the ribosomal L1 stalk three-way junction.Q42244106
Predicting ion-nucleic acid interactions by energy landscape-guided samplingQ42326406
Physics-based de novo prediction of RNA 3D structures.Q42712420
Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamicsQ43152046
The jerky and knotty dynamics of RNA.Q37535132
Multiscale modeling of proteinsQ37604347
Examining the assumptions underlying continuum-solvent modelsQ37684700
Coarse grained models reveal essential contributions of topological constraints to the conformational free energy of RNA bulgesQ37697428
Minimalist models for proteins: a comparative analysisQ37779823
Coarse-grained (multiscale) simulations in studies of biophysical and chemical systemsQ37804856
Predicting RNA folding thermodynamics with a reduced chain representation model.Q43207481
Analysis of relative positions of ribonucleotide bases in a crystal structure of ribosomeQ44223301
All-atom knowledge-based potential for RNA structure prediction and assessmentQ45783105
Coarse-grained simulations of RNA and DNA duplexesQ45894084
Computer modeling 16 S ribosomal RNA.Q46261368
Are mixed explicit/implicit solvation models reliable for studying phosphate hydrolysis? A comparative study of continuum, explicit and mixed solvation modelsQ46457808
Molecular Dynamics and Free Energy Study of the Conformational Equilibria in the UUUU RNA HairpinQ46620443
An all atom force field for simulations of proteins and nucleic acidsQ46625508
The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambinQ47682341
Structural genomics of RNA.Q47809952
Enhanced conformational sampling method for proteins based on the TaBoo SeArch algorithm: application to the folding of a mini-protein, chignolin.Q50957837
GROMACS: A message-passing parallel molecular dynamics implementationQ51756282
ZDOCK: an initial-stage protein-docking algorithm.Q52015255
A novel shape complementarity scoring function for protein‐protein dockingQ52018270
Taboo search: an approach to the multiple minima problem.Q52350711
Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins.Q52451138
Stochastic Relaxation, Gibbs Distributions, and the Bayesian Restoration of ImagesQ52693001
CHARMM: A program for macromolecular energy, minimization, and dynamics calculationsQ53340989
Replica-exchange molecular dynamics method for protein foldingQ55879366
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic MoleculesQ55918670
Future paths for integer programming and links to artificial intelligenceQ55934114
THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The methodQ56157177
Semianalytical treatment of solvation for molecular mechanics and dynamicsQ56866446
Molecular dynamics, Langevin and hydrid Monte Carlo simulations in a multicanonical ensembleQ57906319
Mean-field interactions between nucleic-acid-base dipoles can drive the formation of a double helixQ59278286
Multidimensional free-energy calculations using the weighted histogram analysis methodQ59732710
Optimized Monte Carlo data analysisQ59732808
New Monte Carlo technique for studying phase transitionsQ59732852
Understanding the role of base stacking in nucleic acids. MD and QM analysis of tandem GA base pairs in RNA duplexesQ62140840
Configurational Statistics of Polynucleotide Chains. A Single Virtual Bond TreatmentQ66960592
Spatial configuration of polynucleotide chains. II. Conformational energies and the average dimensions of polyribonucleotidesQ67272566
Spatial configurations of polynucleotide chains. I. Steric interactions in polyribonucleotides: A virtual bond modelQ67272584
Spatial configurations of polynucleotide chains. III. PolydeoxyribonucleotidesQ67272614
Modeling DNA deformationsQ73889040
Taboo search by successive confinement: surveying a potential energy surfaceQ74578516
Theory and applications of the generalized Born solvation model in macromolecular simulationsQ77381573
Rod models of DNA: sequence-dependent anisotropic elastic modelling of local bending phenomenaQ77460955
Structural, mechanical, and thermodynamic properties of a coarse-grained DNA modelQ83503460
Characterization of the mechanical unfolding of RNA pseudoknotsQ28257841
The MC-Fold and MC-Sym pipeline infers RNA structure from sequence dataQ28271703
Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94Q28842789
Critical assessment of methods of protein structure prediction (CASP)--round xQ29048203
An efficient newton-like method for molecular mechanics energy minimization of large moleculesQ29543705
Development and testing of a general amber force fieldQ29547642
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkitQ29615867
A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6Q29617517
Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairsQ29617637
A graph theoretic approach to protein structure selection.Q30372013
RNA and protein 3D structure modeling: similarities and differencesQ30398894
Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluationQ30402159
A graph-theoretic algorithm for comparative modeling of protein structureQ30430781
RNA 3D structure prediction by using a coarse-grained model and experimental dataQ30593882
Predicting RNA 3D structure using a coarse-grain helix-centered modelQ30650995
Describing RNA structure by libraries of clustered nucleotide doubletsQ30788878
Constant-pH molecular dynamics study of protonation-structure relationship in a heptapeptide derived from ovomucoid third domainQ30909689
RNA backbone is rotamericQ31024059
Stepping through an RNA structure: A novel approach to conformational analysisQ31940116
Forced-unfolding and force-quench refolding of RNA hairpinsQ33233771
Comparison of intrinsic stacking energies of ten unique dinucleotide steps in A-RNA and B-DNA duplexes. Can we determine correct order of stability by quantum-chemical calculations?Q33517718
Prediction of RNA multiloop and pseudoknot conformations from a lattice-based, coarse-grain tertiary structure modelQ33538211
New Monte Carlo algorithms for protein folding.Q33632631
Predicting loop-helix tertiary structural contacts in RNA pseudoknotsQ33658469
Multiscale approaches for studying energy transduction in dyneinQ33661160
Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field.Q33726866
ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimersQ33760362
How RNA foldsQ33767912
Mechanical unfolding of RNA hairpinsQ33784317
Atomic accuracy in predicting and designing noncanonical RNA structureQ33789129
On the significance of an RNA tertiary structure predictionQ33913266
Surveying implicit solvent models for estimating small molecule absolute hydration free energiesQ33953525
Fast folding of RNA pseudoknots initiated by laser temperature-jumpQ34035046
Development and current status of the CHARMM force field for nucleic acids.Q34106357
Modeling large RNAs and ribonucleoprotein particles using molecular mechanics techniquesQ34115394
Computational modeling of RNA 3D structures, with the aid of experimental restraintsQ34122757
Escaping free-energy minimaQ34151010
The elastic rod model for DNA and its application to the tertiary structure of DNA minicircles in mononucleosomesQ34167895
Quantum-dynamical picture of a multistep enzymatic process: reaction catalyzed by phospholipase A(2).Q34173784
Multiplexed-replica exchange molecular dynamics method for protein folding simulationQ34180295
Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosomeQ34189280
Modeling nucleic acidsQ34271167
YUP: A Molecular Simulation Program for Coarse-Grained and Multi-Scaled ModelsQ34356303
Properties of the Nucleic-acid Bases in Free and Watson-Crick Hydrogen-bonded States: Computational Insights into the Sequence-dependent Features of Double-helical DNAQ34467021
DNA Duplex Formation with a Coarse-Grained ModelQ34503120
WebRASP: a server for computing energy scores to assess the accuracy and stability of RNA 3D structuresQ34912135
Mapping the kinetic barriers of a Large RNA molecule's folding landscapeQ35105842
RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational spaceQ35222902
RNAcentral: an international database of ncRNA sequencesQ35254982
Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerismQ35382958
Polarizable Atomic Multipole-based Molecular Mechanics for Organic MoleculesQ35385959
RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structuresQ35621422
Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit SolventQ35751959
RNA helix stability in mixed Na+/Mg2+ solutionQ35753774
Modeling and design by hierarchical natural movesQ35779406
RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure predictionQ35853409
Molecular dynamics simulations of RNA: an in silico single molecule approach.Q36058510
Single-molecule mechanical unfolding and folding of a pseudoknot in human telomerase RNA.Q36148350
The role of collective motion in examples of coarsening and self-assembly.Q36452151
Structural inference of native and partially folded RNA by high-throughput contact mappingQ36670098
pH-dependent dynamics of complex RNA macromoleculesQ36697118
Ab initio folding of proteins with all-atom discrete molecular dynamicsQ36870976
Mapping folding energy landscapes with theory and experimentQ36958078
A novel implicit solvent model for simulating the molecular dynamics of RNAQ37145710
Evaluating and learning from RNA pseudotorsional space: quantitative validation of a reduced representation for RNA structureQ37286979
Energy barriers, pathways, and dynamics during folding of large, multidomain RNAsQ37300652
Minimal models for proteins and RNA from folding to functionQ37361859
Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM.Q37366654
Sequence effects in the melting and renaturation of short DNA oligonucleotides: structure and mechanistic pathwaysQ37457152
Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural modelsQ37460103
P407language of work or nameEnglishQ1860
P304page(s)138-56
P577publication date2016-07-01
P1433published inMethodsQ6823859
P1476titleCoarse-grained modeling of RNA 3D structure
P478volume103

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cites work (P2860)
Q640968283D based on 2D: Calculating helix angles and stacking patterns using , an RNA Python library centered on secondary structure elements
Q38857230A coarse-grained model for assisting the investigation of structure and dynamics of large nucleic acids by ion mobility spectrometry-mass spectrometry.
Q63247770Advances in RNA structure determination
Q37744021Capturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations
Q64234069Computational modeling of RNA 3D structure based on experimental data
Q90465256Dual Graph Partitioning Highlights a Small Group of Pseudoknot-Containing RNA Submotifs
Q36140473Electron Transport in a Dioxygenase-Ferredoxin Complex: Long Range Charge Coupling between the Rieske and Non-Heme Iron Center
Q42317200Exploring RNA conformational space under sparse distance restraints
Q47565164F-RAG: Generating Atomic Coordinates from RNA Graphs by Fragment Assembly
Q97520848Free energy-based model of CTCF-mediated chromatin looping in the human genome
Q92235080Inverse folding with RNA-As-Graphs produces a large pool of candidate sequences with target topologies
Q64064419QRNAS: software tool for refinement of nucleic acid structures
Q47235409RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.

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