345 research outputs found
Quantum Chemical Studies Of Nucleic Acids Can We Construct A Bridge To The Rna Structural Biology And Bioinformatics Communities?
In this feature article we provide a side-by-side introduction for two research fields quantum chemical calculations of molecular interaction in nucleic acids and RNA structural bioinformatics Our main aim is to demonstrate that these research areas while largely separated in contemporary literature have substantial potential to complement each other that could significantly contribute to our understanding of the exciting world of nucleic acids We identify research questions amenable to the combined application of modern ab initio methods and bioinformatics analysis of experimental structures while also assessing the limitations of these approaches The ultimate aim is to attain valuable physicochemical insights regarding the nature of the fundamental molecular interactions and how they shape RNA structures, dynamics, function, and evolution
Comprehensive survey and geometric classification of base triples in RNA structures
Base triples are recurrent clusters of three RNA nucleobases interacting edge-to-edge by hydrogen bonding. We find that the central base in almost all triples forms base pairs with the other two bases of the triple, providing a natural way to geometrically classify base triples. Given 12 geometric base pair families defined by the LeontisāWesthof nomenclature, combinatoric enumeration predicts 108 potential geometric base triple families. We searched representative atomic-resolution RNA 3D structures and found instances of 68 of the 108 predicted base triple families. Model building suggests that some of the remaining 40 families may be unlikely to form for steric reasons. We developed an on-line resource that provides exemplars of all base triples observed in the structure database and models for unobserved, predicted triples, grouped by triple family, as well as by three-base combination (http://rna.bgsu.edu/Triples). The classification helps to identify recurrent triple motifs that can substitute for each other while conserving RNA 3D structure, with applications in RNA 3D structure prediction and analysis of RNA sequence evolution
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases
RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences that provides a single access point to 44 RNA resources and >18 million ncRNA sequences from a wide range of organisms and RNA types. RNAcentral now also includes secondary (2D) structure information for >13 million sequences, making RNAcentral the world's largest RNA 2D structure database. The 2D diagrams are displayed using R2DT, a new 2D structure visualization method that uses consistent, reproducible and recognizable layouts for related RNAs. The sequence similarity search has been updated with a faster interface featuring facets for filtering search results by RNA type, organism, source database or any keyword. This sequence search tool is available as a reusable web component, and has been integrated into several RNAcentral member databases, including Rfam, miRBase and snoDB. To allow for a more fine-grained assignment of RNA types and subtypes, all RNAcentral sequences have been annotated with Sequence Ontology terms. The RNAcentral database continues to grow and provide a central data resource for the RNA community
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases.
RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences that provides a single access point to 44 RNA resources and >18 million ncRNA sequences from a wide range of organisms and RNA types. RNAcentral now also includes secondary (2D) structure information for >13 million sequences, making RNAcentral the world's largest RNA 2D structure database. The 2D diagrams are displayed using R2DT, a new 2D structure visualization method that uses consistent, reproducible and recognizable layouts for related RNAs. The sequence similarity search has been updated with a faster interface featuring facets for filtering search results by RNA type, organism, source database or any keyword. This sequence search tool is available as a reusable web component, and has been integrated into several RNAcentral member databases, including Rfam, miRBase and snoDB. To allow for a more fine-grained assignment of RNA types and subtypes, all RNAcentral sequences have been annotated with Sequence Ontology terms. The RNAcentral database continues to grow and provide a central data resource for the RNA community. RNAcentral is freely available at https://rnacentral.org
Complex Random Energy Model: Zeros and Fluctuations
The partition function of the random energy model at inverse temperature
is a sum of random exponentials , where are independent real standard normal random
variables (= random energies), and . We study the large limit of
the partition function viewed as an analytic function of the complex variable
. We identify the asymptotic structure of complex zeros of the partition
function confirming and extending predictions made in the theoretical physics
literature. We prove limit theorems for the random partition function at
complex , both on the logarithmic scale and on the level of limiting
distributions. Our results cover also the case of the sums of independent
identically distributed random exponentials with any given correlations between
the real and imaginary parts of the random exponent.Comment: 31 pages, 1 figur
The Spin Structure of the Nucleon
We present an overview of recent experimental and theoretical advances in our
understanding of the spin structure of protons and neutrons.Comment: 84 pages, 29 figure
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