Global informatics and physical property selection in protein sequences
- 16 February 2016
- journal article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences of the United States of America
- Vol. 113 (7), 1808-1810
- https://doi.org/10.1073/pnas.1525745113
Abstract
The degree of informatic independence between the physical properties of amino acids as encoded in actual protein sequences is calculated. It is shown that no physical property can be identified that carries significantly less information than others and that the information overlap between different properties and different length scales along the sequence is essentially zero. These observations suggest that bioinformatic models based on arbitrarily selected sets of physical properties are inherently deficient.Keywords
Funding Information
- National Insitutes of Health (GM-14312)
- National Science Foundation (MCB-10-19767)
This publication has 13 references indexed in Scilit:
- Nonlinearities in protein space limit the utility of informatics in protein biophysicsProteins-Structure Function and Bioinformatics, 2015
- ProtDCal: A program to compute general-purpose-numerical descriptors for sequences and 3D-structures of proteinsBMC Bioinformatics, 2015
- Fundamentals of Homology Modeling Steps and Comparison among Important Bioinformatics Tools: An OverviewScience International, 2013
- Global characteristics of protein sequences and their implicationsProceedings of the National Academy of Sciences of the United States of America, 2010
- Sequence physical properties encode the global organization of protein structure spaceProceedings of the National Academy of Sciences of the United States of America, 2009
- Characterization of Architecture Signals in ProteinsThe Journal of Physical Chemistry B, 2006
- “Hidden” sequence periodicities and protein architectureProceedings of the National Academy of Sciences of the United States of America, 1998
- On the nature of the protein folding code.Proceedings of the National Academy of Sciences of the United States of America, 1993
- Relation between sequence similarity and structural similarity in proteins. Role of important properties of amino acidsJournal of Protein Chemistry, 1985
- Statistical analysis of the physical properties of the 20 naturally occurring amino acidsProtein Journal, 1985