Literature DB >> 22110566

A brief review of molecular information theory.

Thomas D Schneider1.   

Abstract

The idea that we could build molecular communications systems can be advanced by investigating how actual molecules from living organisms function. Information theory provides tools for such an investigation. This review describes how we can compute the average information in the DNA binding sites of any genetic control protein and how this can be extended to analyze its individual sites. A formula equivalent to Claude Shannon's channel capacity can be applied to molecular systems and used to compute the efficiency of protein binding. This efficiency is often 70% and a brief explanation for that is given. The results imply that biological systems have evolved to function at channel capacity, which means that we should be able to build molecular communications that are just as robust as our macroscopic ones.

Entities:  

Year:  2010        PMID: 22110566      PMCID: PMC3220916          DOI: 10.1016/j.nancom.2010.09.002

Source DB:  PubMed          Journal:  Nano Commun Netw        ISSN: 1878-7789            Impact factor:   2.947


  51 in total

1.  The P1 phage replication protein RepA contacts an otherwise inaccessible thymine N3 proton by DNA distortion or base flipping.

Authors:  I G Lyakhov; P N Hengen; D Rubens; T D Schneider
Journal:  Nucleic Acids Res       Date:  2001-12-01       Impact factor: 16.971

2.  Novel splice site mutation at IVS8 nt 5 of HEXB responsible for a Greek-Cypriot case of Sandhoff disease.

Authors:  K Furihata; A Drousiotou; Y Hara; G Christopoulos; G Stylianidou; V Anastasiadou; I Ueno; P Ioannou
Journal:  Hum Mutat       Date:  1999       Impact factor: 4.878

3.  EcoRI methylase. Physical and catalytic properties of the homogeneous enzyme.

Authors:  R A Rubin; P Modrich
Journal:  J Biol Chem       Date:  1977-10-25       Impact factor: 5.157

4.  Information content of binding sites on nucleotide sequences.

Authors:  T D Schneider; G D Stormo; L Gold; A Ehrenfeucht
Journal:  J Mol Biol       Date:  1986-04-05       Impact factor: 5.469

5.  Using information content and base frequencies to distinguish mutations from genetic polymorphisms in splice junction recognition sites.

Authors:  P K Rogan; T D Schneider
Journal:  Hum Mutat       Date:  1995       Impact factor: 4.878

6.  Quantitative analysis of ribosome binding sites in E.coli.

Authors:  D Barrick; K Villanueba; J Childs; R Kalil; T D Schneider; C E Lawrence; L Gold; G D Stormo
Journal:  Nucleic Acids Res       Date:  1994-04-11       Impact factor: 16.971

7.  Information content of individual genetic sequences.

Authors:  T D Schneider
Journal:  J Theor Biol       Date:  1997-12-21       Impact factor: 2.691

8.  Model of specific complex between catabolite gene activator protein and B-DNA suggested by electrostatic complementarity.

Authors:  I T Weber; T A Steitz
Journal:  Proc Natl Acad Sci U S A       Date:  1984-07       Impact factor: 11.205

9.  Information theory based T7-like promoter models: classification of bacteriophages and differential evolution of promoters and their polymerases.

Authors:  Zehua Chen; Thomas D Schneider
Journal:  Nucleic Acids Res       Date:  2005-10-31       Impact factor: 16.971

10.  Anatomy of Escherichia coli sigma70 promoters.

Authors:  Ryan K Shultzaberger; Zehua Chen; Karen A Lewis; Thomas D Schneider
Journal:  Nucleic Acids Res       Date:  2006-12-22       Impact factor: 16.971

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  16 in total

1.  Intronic sequence elements impede exon ligation and trigger a discard pathway that yields functional telomerase RNA in fission yeast.

Authors:  Ram Kannan; Sean Hartnett; Rodger B Voelker; J Andrew Berglund; Jonathan P Staley; Peter Baumann
Journal:  Genes Dev       Date:  2013-03-06       Impact factor: 11.361

2.  Networking development by Boolean logic.

Authors:  Shikui Tu; Thoru Pederson; Zhiping Weng
Journal:  Nucleus       Date:  2013-02-14       Impact factor: 4.197

3.  Relationship between digital information and thermodynamic stability in bacterial genomes.

Authors:  Dawit Nigatu; Werner Henkel; Patrick Sobetzko; Georgi Muskhelishvili
Journal:  EURASIP J Bioinform Syst Biol       Date:  2016-02-02

4.  Low-Digit and High-Digit Polymers in the Origin of Life.

Authors:  Peter Strazewski
Journal:  Life (Basel)       Date:  2019-02-02

5.  Measuring ambiguity in HLA typing methods.

Authors:  Vanja Paunić; Loren Gragert; Abeer Madbouly; John Freeman; Martin Maiers
Journal:  PLoS One       Date:  2012-08-29       Impact factor: 3.240

6.  TRX-LOGOS - a graphical tool to demonstrate DNA information content dependent upon backbone dynamics in addition to base sequence.

Authors:  Connor H Fortin; Katharina V Schulze; Gregory A Babbitt
Journal:  Source Code Biol Med       Date:  2015-09-25

7.  Context based computational analysis and characterization of ARS consensus sequences (ACS) of Saccharomyces cerevisiae genome.

Authors:  Vinod Kumar Singh; Annangarachari Krishnamachari
Journal:  Genom Data       Date:  2016-07-19

8.  Interdependence, Reflexivity, Fidelity, Impedance Matching, and the Evolution of Genetic Coding.

Authors:  Charles W Carter; Peter R Wills
Journal:  Mol Biol Evol       Date:  2018-02-01       Impact factor: 16.240

9.  Identifying New Small Proteins in Escherichia coli.

Authors:  Caitlin E VanOrsdel; John P Kelly; Brittany N Burke; Christina D Lein; Christopher E Oufiero; Joseph F Sanchez; Larry E Wimmers; David J Hearn; Fatimeh J Abuikhdair; Kathryn R Barnhart; Michelle L Duley; Sarah E G Ernst; Briana A Kenerson; Aubrey J Serafin; Matthew R Hemm
Journal:  Proteomics       Date:  2018-05-02       Impact factor: 3.984

10.  Restriction enzymes use a 24 dimensional coding space to recognize 6 base long DNA sequences.

Authors:  Thomas D Schneider; Vishnu Jejjala
Journal:  PLoS One       Date:  2019-10-31       Impact factor: 3.240

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