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Journal of Chemical Theory and Computation, ISSN 1549-9618, 01/2014, Volume 10, Issue 1, pp. 492 - 499
A necessary step to properly assess and validate the performance of force fields for biomolecules is to exhaustively sample the accessible conformational... 
BIOMOLECULAR SIMULATIONS | AMBER FORCE-FIELD | RESERVOIR | TETRALOOPS | BIOLOGICAL MOLECULES | TORSIONS | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | PREDICTIONS | PARAMETERS | MODEL | EFFICIENCY
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 01/2019, Volume 47, Issue 1, pp. 480 - 494
Abstract Stable RNAs rely on a vast repertoire of long-range interactions to assist in the folding of complex cellular machineries such as the ribosome. The... 
COMPLEX | TERTIARY INTERACTIONS | BIOCHEMISTRY & MOLECULAR BIOLOGY | RNA FOLDING MOTIF | GAAA TETRALOOP | CONSERVED NUCLEOTIDES | EMERGING FIELD | GNRA-TETRALOOP | BINDING-SITE | MODEL | PROTEIN-SYNTHESIS | Structural Biology
Journal Article
RNA, ISSN 1355-8382, 03/2017, Volume 23, Issue 3, pp. 259 - 269
When thinking about RNA three-dimensional structures, coming across GNRA and UNCG tetraloops is perceived as a boon since their folds have been extensively... 
STABILIZE | RECOGNITION | BIOCHEMISTRY & MOLECULAR BIOLOGY | RNA folding | CLASSIFICATION | tetraloop | tRNA anticodon | RIBOSOMAL-RNA | MOTIF | FAMILY | structure prediction | TETRALOOP STRUCTURE | SEQUENCE | NMR STRUCTURE | ANTICODON LOOP | RNA motif
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 09/2016, Volume 12, Issue 9, pp. 4534 - 4548
The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are... 
BASE-PAIRS | TERTIARY INTERACTIONS | PROTEIN | EXPLICIT-SOLVENT | DNA | GNRA TETRALOOP | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | REPLICA-EXCHANGE | PARAMETERS | MOLECULAR-DYNAMICS SIMULATIONS | ENERGY LANDSCAPE | Exchange | Computer simulation | Ribonucleic acids | Computation | Biomolecules | Sampling | Hydrogen bonding | Folding | force field | enhanced sampling methods | REMD | RNA tetraloop | folding
Journal Article
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 6/2016, Volume 113, Issue 24, pp. 6665 - 6670
Journal Article
Molecular Physics, ISSN 0026-8976, 02/2014, Volume 112, Issue 3-4, pp. 379 - 384
Journal Article
Biophysical Journal, ISSN 0006-3495, 07/2017, Volume 113, Issue 2, pp. 313 - 320
Though the structure of the substrate stem loop I (SLI)-stem loop V (SLV) kissing loop junction of the Varkud Satellite ribozyme has been experimentally... 
BIOMOLECULAR SIMULATIONS | AMBER FORCE-FIELD | CONFORMATIONAL-CHANGES | BIOPHYSICS | MAGNESIUM-ION BINDING | NMR STRUCTURE | PARTICLE MESH EWALD | RNA TETRALOOPS | MOLECULAR-DYNAMICS SIMULATIONS | SUBSTRATE RECOGNITION | SELF-CLEAVAGE
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 02/2017, Volume 13, Issue 2, pp. 395 - 399
We proposed a simple van der Waals backbone correction (O2' and OP) to the AMBER ff12 force field in conjunction with the OPC water via an unequal... 
FOLD | METADYNAMICS | MOLECULAR-DYNAMICS | FREE-ENERGY LANDSCAPE | TETRALOOPS | TORSIONS | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | PARAMETERS | SIMULATIONS | PROTEINS | WATER | Backbone | Stability | Ribonucleic acids | Computation | Process control
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 02/2017, Volume 13, Issue 2, pp. 900 - 915
The backbone dihedral parameters of the Amber RNA force field were improved by fitting using multiple linear regression to potential energies determined by... 
A-RNA | DNA OLIGONUCLEOTIDES | SIDE-CHAIN | TETRALOOPS | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | NUCLEIC-ACID STRUCTURES | CHEMISTRY, PHYSICAL | GA PAIRS | SIMULATIONS | UNIQUE TETRANUCLEOTIDE SEQUENCES | DENSITY-FUNCTIONAL THEORY | BACKBONE PARAMETERS
Journal Article
by Yang, C and Kulkarni, M and Lim, M and Pak, Y
NUCLEIC ACIDS RESEARCH, ISSN 0305-1048, 12/2017, Volume 45, Issue 22, pp. 12648 - 12656
The reversible folding of the thrombin-binding DNA aptamer G-quadruplexes (GQs) (TBA-15) starting from fully unfolded states was demonstrated using a prolonged... 
BIOMOLECULAR SIMULATIONS | TELOMERIC G-QUADRUPLEXES | AMBER FORCE-FIELD | MONOVALENT ION PARAMETERS | BETA-HAIRPIN | FREE-ENERGY LANDSCAPE | BIOCHEMISTRY & MOLECULAR BIOLOGY | DNA APTAMER | RNA TETRALOOPS | MOLECULAR-DYNAMICS SIMULATIONS | NUCLEIC-ACIDS | Computational Biology
Journal Article
Journal of the American Chemical Society, ISSN 0002-7863, 12/2017, Volume 139, Issue 51, pp. 18576 - 18589
Decades of study of the RNA folding problem have revealed that diverse and complex structured RNAs are built from a common set of recurring structural motifs,... 
P4-P6 RNA | ANGSTROM RESOLUTION | STRUCTURAL ENSEMBLES | LARGE RIBOSOMAL-SUBUNIT | ACID ION ATMOSPHERE | TETRALOOP-RECEPTOR | GAAA TETRALOOP | TRANSITION-STATE | THERMODYNAMIC FRAMEWORK | CHEMISTRY, MULTIDISCIPLINARY | NUCLEIC-ACIDS | Chemical properties | RNA | Chemical reaction, Rate of | Structure | Hydrogen bonding | Analysis
Journal Article
Journal Article
The journal of physical chemistry. B, ISSN 1520-6106, 10/2017, Volume 121, Issue 39, pp. 9175 - 9184
We report the thermodynamic contributions of loop length and loop sequence to the overall stability of DNA intramolecular pyrimidine triplexes. Two sets of... 
ENTHALPY-ENTROPY COMPENSATIONS | DUPLEX STABILITY | THERMODYNAMICS | GNRA | SIZE | DYNAMICS | CHEMISTRY, PHYSICAL | HELIX | RNA TETRALOOPS | HAIRPIN LOOPS | NUCLEIC-ACIDS | Thermodynamics | DNA - chemistry | Genes, tat | DNA Sequence, Unstable | Pyrimidines - chemistry | Usage | Pyrimidines | Research | Chemical properties | Genetic regulation | Enthalpy
Journal Article