Document Detail


Evaluating mixture models for building RNA knowledge-based potentials.
MedLine Citation:
PMID:  22809345     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Ribonucleic acid (RNA) molecules play important roles in a variety of biological processes. To properly function, RNA molecules usually have to fold to specific structures, and therefore understanding RNA structure is vital in comprehending how RNA functions. One approach to understanding and predicting biomolecular structure is to use knowledge-based potentials built from experimentally determined structures. These types of potentials have been shown to be effective for predicting both protein and RNA structures, but their utility is limited by their significantly rugged nature. This ruggedness (and hence the potential's usefulness) depends heavily on the choice of bin width to sort structural information (e.g. distances) but the appropriate bin width is not known a priori. To circumvent the binning problem, we compared knowledge-based potentials built from inter-atomic distances in RNA structures using different mixture models (Kernel Density Estimation, Expectation Minimization and Dirichlet Process). We show that the smooth knowledge-based potential built from Dirichlet process is successful in selecting native-like RNA models from different sets of structural decoys with comparable efficacy to a potential developed by spline-fitting - a commonly taken approach - to binned distance histograms. The less rugged nature of our potential suggests its applicability in diverse types of structural modeling.
Authors:
Adelene Y L Sim; Olivier Schwander; Michael Levitt; Julie Bernauer
Related Documents :
1350255 - Evidence for different neurochemical contributions to long-term potentiation and to kin...
20345515 - Use of mouse models to study the mechanisms and consequences of rbc clearance.
22249925 - A new model for breaking bad news to people with intellectual disabilities.
20211655 - Behavioral phenotyping of mouse models of parkinson's disease.
24099845 - Non-gaussian methods and high-pass filters in the estimation of effective connections.
24808045 - A scalable stagewise approach to large-margin multiclass loss-based boosting.
Publication Detail:
Type:  Evaluation Studies; Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.    
Journal Detail:
Title:  Journal of bioinformatics and computational biology     Volume:  10     ISSN:  0219-7200     ISO Abbreviation:  J Bioinform Comput Biol     Publication Date:  2012 Apr 
Date Detail:
Created Date:  2012-07-19     Completed Date:  2012-11-19     Revised Date:  2014-06-03    
Medline Journal Info:
Nlm Unique ID:  101187344     Medline TA:  J Bioinform Comput Biol     Country:  England    
Other Details:
Languages:  eng     Pagination:  1241010     Citation Subset:  IM    
Export Citation:
APA/MLA Format     Download EndNote     Download BibTex
MeSH Terms
Descriptor/Qualifier:
Computational Biology / methods*
Knowledge Bases
Models, Molecular
RNA / chemistry*,  metabolism
Grant Support
ID/Acronym/Agency:
GM063817/GM/NIGMS NIH HHS; R01 GM063817/GM/NIGMS NIH HHS
Chemical
Reg. No./Substance:
63231-63-0/RNA
Comments/Corrections

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


Previous Document:  VirE2-DEPENDENT PORES FOR ssDNA TRANSFER ACROSS ARTIFICIAL AND CELL MEMBRANES.
Next Document:  Flexible and robust networks.