Next Article in Journal / Special Issue
Security of the Bennett-Brassard Quantum Key Distribution Protocol against Collective Attacks
Previous Article in Journal
Probabilistic Upscaling of Material Failure Using Random Field Models – A Preliminary Investigation
Previous Article in Special Issue
Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams and String Descriptors
Algorithms 2009, 2(2), 764-789; doi:10.3390/a2020764
Article

SDPhound, a Mutual Information-Based Method to Investigate Specificity-Determining Positions

1, †, ‡
, 1, 2, †,* , 1
, 1
 and 1
Received: 22 December 2008; in revised form: 12 March 2009 / Accepted: 5 May 2009 / Published: 26 May 2009
(This article belongs to the Special Issue Algorithms and Molecular Sciences)
Download PDF [1452 KB, uploaded 26 May 2009]
Abstract: Considerable importance in molecular biophysics is attached to influencing by mutagenesis the specific properties of a protein family. The working hypothesis is that mutating residues at few selected positions can affect specificity. Statistical analysis of homologue sequences can identify putative specificity determining positions (SDPs) and help to shed some light on the peculiarities underlying their functional role. In this work, we present an approach to identify such positions inspired by state of the art mutual information-based SDP prediction methods. The algorithm based on this approach provides a systematic procedure to point at the relevant physical characteristics of putative SPDs and can investigate the effects of correlated mutations. The method is tested on two standard benchmarks in the field and further validated in the context of a biologically interesting problem: the multimerization of the Intrinsically Fluorescent Proteins (IFP).
Keywords: specificity determining positions; intrinsically fluorescent proteins; mutual information specificity determining positions; intrinsically fluorescent proteins; mutual information
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Export to BibTeX |
EndNote


MDPI and ACS Style

Bonella, S.; Rocchia, W.; Amat, P.; Nifosí, R.; Tozzini, V. SDPhound, a Mutual Information-Based Method to Investigate Specificity-Determining Positions. Algorithms 2009, 2, 764-789.

AMA Style

Bonella S, Rocchia W, Amat P, Nifosí R, Tozzini V. SDPhound, a Mutual Information-Based Method to Investigate Specificity-Determining Positions. Algorithms. 2009; 2(2):764-789.

Chicago/Turabian Style

Bonella, Sara; Rocchia, Walter; Amat, Pietro; Nifosí, Riccardo; Tozzini, Valentina. 2009. "SDPhound, a Mutual Information-Based Method to Investigate Specificity-Determining Positions." Algorithms 2, no. 2: 764-789.


Algorithms EISSN 1999-4893 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert