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Title: Apparatus and method for determining microscale interactions based on compressive sensors such as crystal structures

Abstract

Techniques for determining values for a metric of microscale interactions include determining a mesoscale metric for a plurality of mesoscale interaction types, wherein a value of the mesoscale metric for each mesoscale interaction type is based on a corresponding function of values of the microscale metric for the plurality of the microscale interaction types. A plurality of observations that indicate the values of the mesoscale metric are determined for the plurality of mesoscale interaction types. Values of the microscale metric are determined for the plurality of microscale interaction types based on the plurality of observations and the corresponding functions and compressed sensing.

Inventors:
;
Issue Date:
Research Org.:
The Board of Trustees of the Leland Stanford Jr. University, Palo Alto, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1178238
Patent Number(s):
9,014,988
Application Number:
13/426,824
Assignee:
The Board of Trustees of the Leland Stanford Jr. University (Palo Alto, CA)
DOE Contract Number:  
FG02-05ER64136
Resource Type:
Patent
Resource Relation:
Patent File Date: 2012 Mar 22
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES; 47 OTHER INSTRUMENTATION

Citation Formats

McAdams, Harley, and AlQuraishi, Mohammed. Apparatus and method for determining microscale interactions based on compressive sensors such as crystal structures. United States: N. p., 2015. Web.
McAdams, Harley, & AlQuraishi, Mohammed. Apparatus and method for determining microscale interactions based on compressive sensors such as crystal structures. United States.
McAdams, Harley, and AlQuraishi, Mohammed. Tue . "Apparatus and method for determining microscale interactions based on compressive sensors such as crystal structures". United States. https://www.osti.gov/servlets/purl/1178238.
@article{osti_1178238,
title = {Apparatus and method for determining microscale interactions based on compressive sensors such as crystal structures},
author = {McAdams, Harley and AlQuraishi, Mohammed},
abstractNote = {Techniques for determining values for a metric of microscale interactions include determining a mesoscale metric for a plurality of mesoscale interaction types, wherein a value of the mesoscale metric for each mesoscale interaction type is based on a corresponding function of values of the microscale metric for the plurality of the microscale interaction types. A plurality of observations that indicate the values of the mesoscale metric are determined for the plurality of mesoscale interaction types. Values of the microscale metric are determined for the plurality of microscale interaction types based on the plurality of observations and the corresponding functions and compressed sensing.},
doi = {},
journal = {},
number = ,
volume = ,
place = {United States},
year = {2015},
month = {4}
}

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Works referenced in this record:

An all-atom, distance-dependent scoring function for the prediction of protein-DNA interactions from structure
journal, October 2006

  • Robertson, Timothy A.; Varani, Gabriele
  • Proteins: Structure, Function, and Bioinformatics, Vol. 66, Issue 2
  • DOI: 10.1002/prot.21162

Identification of rare alleles and their carriers using compressed se(que)nsing
journal, August 2010

  • Shental, N.; Amir, A.; Zuk, O.
  • Nucleic Acids Research, Vol. 38, Issue 19
  • DOI: 10.1093/nar/gkq675

Prediction of TF target sites based on atomistic models of protein-DNA complexes
journal, October 2008

  • Angarica, Vladimir Espinosa; Pérez, Abel González; Vasconcelos, Ana T.
  • BMC Bioinformatics, Vol. 9, Issue 1
  • DOI: 10.1186/1471-2105-9-436

Quantitative Robust Uncertainty Principles and Optimally Sparse Decompositions
journal, December 2005

  • Candes, Emmanuel J.; Romberg, Justin
  • Foundations of Computational Mathematics, Vol. 6, Issue 2
  • DOI: 10.1007/s10208-004-0162-x

The Dantzig selector: Statistical estimation when p is much larger than n
journal, December 2007


Exact Matrix Completion via Convex Optimization
journal, April 2009

  • Candès, Emmanuel J.; Recht, Benjamin
  • Foundations of Computational Mathematics, Vol. 9, Issue 6
  • DOI: 10.1007/s10208-009-9045-5

A Probabilistic and RIPless Theory of Compressed Sensing
journal, November 2011

  • Candes, Emmanuel J.; Plan, Yaniv
  • IEEE Transactions on Information Theory, Vol. 57, Issue 11
  • DOI: 10.1109/TIT.2011.2161794

Energetics of protein–DNA interactions
journal, January 2007

  • Donald, Jason E.; Chen, William W.; Shakhnovich, Eugene I.
  • Nucleic Acids Research, Vol. 35, Issue 4
  • DOI: 10.1093/nar/gkl1103

Regularization Paths for Generalized Linear Models via Coordinate Descent
journal, January 2010

  • Friedman, Jerome; Hastie, Trevor; Tibshirani, Robert
  • Journal of Statistical Software, Vol. 33, Issue 1
  • DOI: 10.18637/jss.v033.i01

A generalized Dantzig selector with shrinkage tuning
journal, May 2009


Protein-DNA binding specificity predictions with structural models
journal, October 2005


Connecting protein structure with predictions of regulatory sites
journal, April 2007

  • Morozov, A. V.; Siggia, E. D.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 17, p. 7068-7073
  • DOI: 10.1073/pnas.0701356104

Regression shrinkage and selection via the lasso: a retrospective: Regression Shrinkage and Selection via the Lasso
journal, April 2011


On the conditioning of random subdictionaries
journal, July 2008