Results 41 to 50 of about 34,544 (276)

Improving model predictions for RNA interference activities that use support vector machine regression by combining and filtering features

BMC Bioinformatics, 2007
Background RNA interference (RNAi) is a naturally occurring phenomenon that results in the suppression of a target RNA sequence utilizing a variety of possible methods and pathways.
Peek Andrew S
doaj   +1 more source

Modified RNA triplexes: Thermodynamics, structure and biological potential

Scientific Reports, 2018
The occurrence of triplexes in vivo has been well documented and is determined by the presence of long homopurine-homopyrimidine tracts. The formation of these structures is the result of conformational changes that occur in the duplex, which allow the ...
Marta Szabat, Elzbieta Kierzek, Ryszard Kierzek   +2 more
doaj   +1 more source

Ab initio RNA folding

, 2014
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray crystallography and
Cragnolini, Tristan, Derreumaux, Philippe, Pasquali, Samuela   +2 more
core   +1 more source

Force-induced misfolding in RNA [PDF]

, 2009
RNA folding is a kinetic process governed by the competition of a large number of structures stabilized by the transient formation of base pairs that may induce complex folding pathways and the formation of misfolded structures. Despite of its importance
D. Herschlag, F. Ritort, I. Junier, I. Tinoco, Jr., M. Manosas, P. J. Flory   +5 more
core   +3 more sources

Changes in Thermodynamic Parameters Induced by Pyrimidine Nucleic Bases Forming Complexes with Amino Acids and Peptides in a Buffer Solution at pH = 7.4

Liquids
This article presents a mini-review of the available data on the thermodynamics of the complexation of amino acids and peptides with some nucleic bases in a buffer medium.
Elena Yu. Tyunina, Vladimir P. Barannikov, Igor N. Mezhevoi   +2 more
doaj   +1 more source

ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions [PDF]

Nucleic Acids Research, 2006
ProTherm and ProNIT are two thermodynamic databases that contain experimentally determined thermodynamic parameters of protein stability and protein-nucleic acid interactions, respectively. The current versions of both the databases have considerably increased the total number of entries and enhanced search interface with added new fields, improved ...
K. Abdulla Bava, Koji Kitajima, Hatsuho Uedaira, M. D. Shaji Kumar, Ponraj Prabakaran, M. Michael Gromiha, Akinori Sarai   +6 more
openaire   +3 more sources

Coarse-grained simulations of RNA and DNA duplexes

, 2013
Although RNAs play many cellular functions little is known about the dynamics and thermodynamics of these molecules. In principle, all-atom molecular dynamics simulations can investigate these issues, but with current computer facilities, these ...
Cragnolini, Tristan, Derreumaux, Philippe, Pasquali, Samuela   +2 more
core   +1 more source

Genome-scale architecture of small molecule regulatory networks and the fundamental trade-off between regulation and enzymatic activity [PDF]

, 2017
Metabolic flux is in part regulated by endogenous small molecules that modulate the catalytic activity of an enzyme, e.g., allosteric inhibition. In contrast to transcriptional regulation of enzymes, technical limitations have hindered the production of ...
Briars, Emma, Christodoulou, Dimitris, Goldford, Joshua E., Noor, Elad, Reznik, Ed, Sauer, Uwe, Segrè, Daniel   +6 more
core   +2 more sources

Consolidate Overview of Ribonucleic Acid Molecular Dynamics: From Molecular Movements to Material Innovations

Advanced Engineering Materials, EarlyView.
Molecular dynamics simulations are advancing the study of ribonucleic acid (RNA) and RNA‐conjugated molecules. These developments include improvements in force fields, long‐timescale dynamics, and coarse‐grained models, addressing limitations and refining methods.
Kanchan Yadav, Iksoo Jang, Jong Bum Lee
wiley   +1 more source

An O(n^5) algorithm for MFE prediction of kissing hairpins and 4-chains in nucleic acids [PDF]

, 2008
Efficient methods for prediction of minimum free energy (MFE) nucleic secondary structures are widely used, both to better understand structure and function of biological RNAs and to design novel nano-structures.
Chen, Ho-Lin, Condon, Anne, Jabbari, Hosna   +2 more
core   +3 more sources