Parisien M, Cruz J A, Westhof E, Major F
New metrics for comparing and assessing discrepancies between RNA 3D structures and models Article de journal
Dans: RNA, vol. 15, no. 10, p. 1875-1885, 2009, ISBN: 19710185, (1469-9001 (Electronic) 1355-8382 (Linking) Comparative Study Journal Article Research Support, Non-U.S. Gov't).
Résumé | Liens | BibTeX | Étiquettes: 28S/*chemistry Rats, Animals Base Pairing Calibration *Models, Molecular *Nucleic Acid Conformation RNA, Ribosomal, Unité ARN, WESTHOF
@article{,
title = {New metrics for comparing and assessing discrepancies between RNA 3D structures and models},
author = {M Parisien and J A Cruz and E Westhof and F Major},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19710185},
isbn = {19710185},
year = {2009},
date = {2009-01-01},
journal = {RNA},
volume = {15},
number = {10},
pages = {1875-1885},
abstract = {To benchmark progress made in RNA three-dimensional modeling and assess newly developed techniques, reliable and meaningful comparison metrics and associated tools are necessary. Generally, the average root-mean-square deviations (RMSDs) are quoted. However, RMSD can be misleading since errors are spread over the whole molecule and do not account for the specificity of RNA base interactions. Here, we introduce two new metrics that are particularly suitable to RNAs: the deformation index and deformation profile. The deformation index is calibrated by the interaction network fidelity, which considers base-base-stacking and base-base-pairing interactions within the target structure. The deformation profile highlights dissimilarities between structures at the nucleotide scale for both intradomain and interdomain interactions. Our results show that there is little correlation between RMSD and interaction network fidelity. The deformation profile is a tool that allows for rapid assessment of the origins of discrepancies.},
note = {1469-9001 (Electronic)
1355-8382 (Linking)
Comparative Study
Journal Article
Research Support, Non-U.S. Gov't},
keywords = {28S/*chemistry Rats, Animals Base Pairing Calibration *Models, Molecular *Nucleic Acid Conformation RNA, Ribosomal, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Leontis N B, Stombaugh J, Westhof E
Motif prediction in ribosomal RNAs Lessons and prospects for automated motif prediction in homologous RNA molecules Article de journal
Dans: Biochimie, vol. 84, no. 9, p. 961-973, 2002, ISBN: 12458088, (0300-9084 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Bacterial/*chemistry/genetics RNA, Base Pairing Base Sequence Catalytic Domain Conserved Sequence Databases, Factual Models, Molecular *Nucleic Acid Conformation RNA, Non-P.H.S. Support, P.H.S., Ribosomal/*chemistry/genetics Sequence Alignment Support, U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {Motif prediction in ribosomal RNAs Lessons and prospects for automated motif prediction in homologous RNA molecules},
author = {N B Leontis and J Stombaugh and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12458088},
isbn = {12458088},
year = {2002},
date = {2002-01-01},
journal = {Biochimie},
volume = {84},
number = {9},
pages = {961-973},
abstract = {The traditional way to infer RNA secondary structure involves an iterative process of alignment and evaluation of covariation statistics between all positions possibly involved in basepairing. Watson-Crick basepairs typically show covariations that score well when examples of two or more possible basepairs occur. This is not necessarily the case for non-Watson-Crick basepairing geometries. For example, for sheared (trans Hoogsteen/Sugar edge) pairs, one base is highly conserved (always A or mostly A with some C or U), while the other can vary (G or A and sometimes C and U as well). RNA motifs consist of ordered, stacked arrays of non-Watson-Crick basepairs that in the secondary structure representation form hairpin or internal loops, multi-stem junctions, and even pseudoknots. Although RNA motifs occur recurrently and contribute in a modular fashion to RNA architecture, it is usually not apparent which bases interact and whether it is by edge-to-edge H-bonding or solely by stacking interactions. Using a modular sequence-analysis approach, recurrent motifs related to the sarcin-ricin loop of 23S RNA and to loop E from 5S RNA were predicted in universally conserved regions of the large ribosomal RNAs (16S- and 23S-like) before the publication of high-resolution, atomic-level structures of representative examples of 16S and 23S rRNA molecules in their native contexts. This provides the opportunity to evaluate the predictive power of motif-level sequence analysis, with the goal of automating the process for predicting RNA motifs in genomic sequences. The process of inferring structure from sequence by constructing accurate alignments is a circular one. The crucial link that allows a productive iteration of motif modeling and realignment is the comparison of the sequence variations for each putative pair with the corresponding isostericity matrix to determine which basepairs are consistent both with the sequence and the geometrical data.},
note = {0300-9084
Journal Article},
keywords = {Bacterial/*chemistry/genetics RNA, Base Pairing Base Sequence Catalytic Domain Conserved Sequence Databases, Factual Models, Molecular *Nucleic Acid Conformation RNA, Non-P.H.S. Support, P.H.S., Ribosomal/*chemistry/genetics Sequence Alignment Support, U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Auffinger P, Westhof E
H-bond stability in the tRNA(Asp) anticodon hairpin: 3 ns of multiple molecular dynamics simulations Article de journal
Dans: Biophys J, vol. 71, no. 2, p. 940-954, 1996, ISBN: 8842234, (0006-3495 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anticodon/*chemistry Base Composition Base Sequence *Computer Simulation Drug Stability Hydrogen Bonding Kinetics Models, Asp/*chemistry Software Support, Molecular *Nucleic Acid Conformation RNA, Non-U.S. Gov't, Transfer, Unité ARN
@article{,
title = {H-bond stability in the tRNA(Asp) anticodon hairpin: 3 ns of multiple molecular dynamics simulations},
author = {P Auffinger and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8842234},
isbn = {8842234},
year = {1996},
date = {1996-01-01},
journal = {Biophys J},
volume = {71},
number = {2},
pages = {940-954},
abstract = {Multiple molecular dynamics trajectories of the solvated and neutralized 17-residue tRNA(Asp) anticodon hairpin were generated for a total of 3 ns. Explicit treatment of all long-ranged electrostatic interactions by the particle mesh Ewald algorithm, as implemented in the AMBER MD software package, effected a degree of structural stabilization not previously achieved by use of a long 16-A solvent interaction truncation scheme. The increased stability of this multiple molecular dynamics set was appropriate for an in-depth analysis of the six 500-ps-long trajectories and allowed the characterization of a number of key structural interactions. The dynamical behavior of the standard Watson-Crick base pairs, the noncanonical G30-U40 "wobble" base pair, and the psi 32-C38 pseudo-base pair is presented as well as that of two C--H. O hydrogen bonds found to contribute to the array of tertiary interactions that stabilize the seven-nucleotide native loop conformation. The least mobile residue in the loop is U33, which forms the U-turn motif and which participates in several hydrogen-bonding interactions, whereas the most mobile residue is the apical residue G34 at the wobble position, a factor undoubtedly important in its biological function. The set of multiple molecular dynamics trajectories obtained does not converge on a 500-ps time scale to a unique dynamical model but instead describes an ensemble of structural microstates accessible to the system under the present simulation protocol, which is the result of local structural heterogeneity rather than of global conformational changes.},
note = {0006-3495
Journal Article},
keywords = {Anticodon/*chemistry Base Composition Base Sequence *Computer Simulation Drug Stability Hydrogen Bonding Kinetics Models, Asp/*chemistry Software Support, Molecular *Nucleic Acid Conformation RNA, Non-U.S. Gov't, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}