Using relative entropy to find optimal approximations: An application to simple fluids

Tseng, Chih‐Yuan; Caticha, Ariel

doi:10.1016/j.physa.2008.08.035

Cited by 11 publications

(15 citation statements)

References 42 publications

(43 reference statements)

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“…The key to this approach lies in answering the question: ‘Given the structural information of the target, what is the preferred probability distribution of having an aptamer that is most likely to interact with the target?’ We propose to integrate the concept of information processing with the seed‐and‐grow strategy to answer this question and design templates for aptamers. Three methods regarding information processing are considered: (i) a method of assigning probability distributions based on a limited amount of information denoted by MaxEnt (10,11); (ii) a method of updating probability distributions from a priori when new information becomes available denoted by ME (12–15); and (iii) a selection criterion for different probability distributions associated with various types of nucleotides (16–18).…”

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confidence: 99%

Entropic Fragment‐Based Approach to Aptamer Design

Tseng¹,

Ashrafuzzaman

Mane

et al. 2011

Chem Biol Drug Des

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Aptamers are short RNA ⁄ DNA sequences that are identified through the process of systematic evolution of ligands by exponential enrichment and that bind to diverse biomolecular targets. Aptamers have strong and specific binding through molecular recognition and are promising tools in studying molecular biology. They are recognized as having potential therapeutic and diagnostic clinical applications. The success of the systematic evolution of ligands by exponential enrichment process requires that the RNA ⁄ DNA pools used in the process have a sufficient level of sequence diversity and structural complexity. While the systematic evolution of ligands by exponential enrichment technology is well developed, it remains a challenge in the efficient identification of correct aptamers. In this article, we propose a novel information-driven approach to a theoretical design of aptamer templates based solely on the knowledge regarding the biomolecular target structures. We have investigated both theoretically and experimentally the applicability of the proposed approach by considering two specific targets: the serum protein thrombin and the cell membrane phospholipid phosphatidylserine. Both of these case studies support our method and indicate a promising advancement in theoretical aptamer design. In unfavorable cases where the designed sequences show weak binding affinity, these template sequences can be still modified to enhance their affinities without going through the systematic evolution of ligands by exponential enrichment process.Key words: bioinformatics, mechanism-based drug design, molecular recognition, structure-based drug design Received 18 October 2010, revised 24 February 2011 and accepted for publication 1 April 2011 Aptamers, short RNA ⁄ DNA sequences, are selected through an experimental technique known as systematic evolution of ligands by exponential enrichment (SELEX) to bind to specific biomolecular targets including small molecules, proteins, nucleic acids, phospholipids as well as complex structures such as cells, tissues, bacteria, and other organisms. Aptamers have strong and specific binding through molecular recognition and are promising tools in studying molecular biology with recognized therapeutic and diagnostic clinical applications (1-5). SELEX consists of a number of rounds of in vitro selection in which the RNA ⁄ DNA pool is incubated with the binding target. The non-binding or loosely binding sequences are discarded, while the binding sequences are expanded using the polymerase chain reaction method to provide a pool of sequences for the next round of testing. In practice, multiple rounds of selection and expansion are required before unique tightly binding sequences can be identified. Additionally, isolated aptamers will often need to be reengineered to reduce their sequence length and impart additional favorable biological properties. These issues pose a challenge for the efficient identification of correct aptamers.Over the past several years, various research groups have attempted...

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confidence: 99%

Entropic Fragment‐Based Approach to Aptamer Design

Tseng¹,

Ashrafuzzaman

Mane

et al. 2011

Chem Biol Drug Des

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“…This disagreement is due to an assumed consistency of approximations. In Reference [13], further approximations are forced to be consistent with earlier approximations; i.e., if one does two approximations, one gets the same result as with one joint approximation. Due to this requirement, the derived functional cannot satisfy some of the axioms that we used.…”

Section: Discussionmentioning

confidence: 99%

Optimal Belief Approximation

Leike

Enßlin

2017

Entropy

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Abstract:In Bayesian statistics probability distributions express beliefs. However, for many problems the beliefs cannot be computed analytically and approximations of beliefs are needed. We seek a loss function that quantifies how "embarrassing" it is to communicate a given approximation. We reproduce and discuss an old proof showing that there is only one ranking under the requirements that (1) the best ranked approximation is the non-approximated belief and (2) that the ranking judges approximations only by their predictions for actual outcomes. The loss function that is obtained in the derivation is equal to the Kullback-Leibler divergence when normalized. This loss function is frequently used in the literature. However, there seems to be confusion about the correct order in which its functional arguments-the approximated and non-approximated beliefs-should be used. The correct order ensures that the recipient of a communication is only deprived of the minimal amount of information. We hope that the elementary derivation settles the apparent confusion. For example when approximating beliefs with Gaussian distributions the optimal approximation is given by moment matching. This is in contrast to many suggested computational schemes.

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“…This approach is free from some of the impediments of SELEX as mentioned above. Regarding aptamer design the detailed method of maximum entropy is described in [ 60 – 68 ]. I wish to provide here brief description on our novel technique applied for aptamer design (for details see [ 11 , 38 ]).…”

Section: Aptamer Designing Templatesmentioning

confidence: 99%

Aptamers as Both Drugs and Drug-Carriers

Ashrafuzzaman

2014

BioMed Research International

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Aptamers are short nucleic acid oligos. They may serve as both drugs and drug-carriers. Their use as diagnostic tools is also evident. They can be generated using various experimental, theoretical, and computational techniques. The systematic evolution of ligands by exponential enrichment which uses iterative screening of nucleic acid libraries is a popular experimental technique. Theory inspired methodology entropy-based seed-and-grow strategy that designs aptamer templates to bind specifically to targets is another one. Aptamers are predicted to be highly useful in producing general drugs and theranostic drugs occasionally for certain diseases like cancer, Alzheimer's disease, and so on. They bind to various targets like lipids, nucleic acids, proteins, small organic compounds, and even entire organisms. Aptamers may also serve as drug-carriers or nanoparticles helping drugs to get released in specific target regions. Due to better target specific physical binding properties aptamers cause less off-target toxicity effects. Therefore, search for aptamer based drugs, drug-carriers, and even diagnostic tools is expanding fast. The biophysical properties in relation to the target specific binding phenomena of aptamers, energetics behind the aptamer transport of drugs, and the consequent biological implications will be discussed. This review will open up avenues leading to novel drug discovery and drug delivery.

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Using relative entropy to find optimal approximations: An application to simple fluids

Cited by 11 publications

References 42 publications

Entropic Fragment‐Based Approach to Aptamer Design

Entropic Fragment‐Based Approach to Aptamer Design

Optimal Belief Approximation

Aptamers as Both Drugs and Drug-Carriers

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