Document Detail


Application of new multi-resolution methods for the comparison of biomolecular electrostatic properties in the absence of global structural similarity.
MedLine Citation:
PMID:  18841247     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
In this paper we present a method for the multi-resolution comparison of biomolecular electrostatic potentials without the need for global structural alignment of the biomolecules. The underlying computational geometry algorithm uses multi-resolution attributed contour trees (MACTs) to compare the topological features of volumetric scalar fields. We apply the MACTs to compute electrostatic similarity metrics for a large set of protein chains with varying degrees of sequence, structure, and function similarity. For calibration, we also compute similarity metrics for these chains by a more traditional approach based upon 3D structural alignment and analysis of Carbo similarity indices. Moreover, because the MACT approach does not rely upon pairwise structural alignment, its accuracy and efficiency promises to perform well on future large-scale classification efforts across groups of structurally-diverse proteins. The MACT method discriminates between protein chains at a level comparable to the Carbo similarity index method; i.e., it is able to accurately cluster proteins into functionally-relevant groups which demonstrate strong dependence on ligand binding sites. The results of the analyses are available from the linked web databases http://ccvweb.cres.utexas.edu/MolSignature/ and http://agave.wustl.edu/similarity/. The MACT analysis tools are available as part of the public domain library of the Topological Analysis and Quantitative Tools (TAQT) from the Center of Computational Visualization, at the University of Texas at Austin (http://ccvweb.csres.utexas.edu/software). The Carbo software is available for download with the open-source APBS software package at http://apbs.sf.net/.
Authors:
Xiaoyu Zhang; Chandrajit L Bajaj; Bongjune Kwon; Todd J Dolinsky; Jens E Nielsen; Nathan A Baker
Related Documents :
20158037 - Hierarchical coarse-graining strategy for protein-membrane systems to access mesoscopic...
12217917 - Esypred3d: prediction of proteins 3d structures.
22654177 - A database of computational models of a half-center oscillator for analyzing how neuron...
9741857 - Regression spline models and model calibration in the identification of protein storage...
19455357 - Conformism in the food processing techniques of white-faced capuchin monkeys (cebus cap...
20879337 - Shell model for reconstruction and real-time simulation of thin anatomical structures.
Publication Detail:
Type:  JOURNAL ARTICLE    
Journal Detail:
Title:  Multiscale modeling & simulation : a SIAM interdisciplinary journal     Volume:  5     ISSN:  -     ISO Abbreviation:  Multiscale Model Simul     Publication Date:  2006  
Date Detail:
Created Date:  2009-3-5     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  101480165     Medline TA:  Multiscale Model Simul     Country:  -    
Other Details:
Languages:  ENG     Pagination:  1196-1213     Citation Subset:  -    
Affiliation:
Department of Computer Science, California State University San Marcos, 333 S. Twin Oaks Valley Road, San Marcos, CA 92096. , , E-mail: xiaoyu@csusm.edu.
Export Citation:
APA/MLA Format     Download EndNote     Download BibTex
MeSH Terms
Descriptor/Qualifier:
Grant Support
ID/Acronym/Agency:
R01 GM069702-01//NIGMS NIH HHS; R01 GM069702-02//NIGMS NIH HHS; R01 GM069702-03//NIGMS NIH HHS; R01 GM069702-04//NIGMS NIH HHS

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


Previous Document:  THE RACE/ETHNICITY DISPARITY IN MISDEMEANOR MARIJUANA ARRESTS IN NEW YORK CITY.
Next Document:  ANOPTIMAL DELIVERYFORMATFORPRESENTATIONS TARGETINGOLDER ADULTS.