Algorithms 2009, 2(2), 764-789; doi:10.3390/a2020764
Article

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

Sara Bonella 1, †, ‡ email, Walter Rocchia 1, 2, †,* email, Pietro Amat 1 email, Riccardo Nifosí 1 email and Valentina Tozzini 1 email
1 NEST Scuola Normale Superiore and CNR-INFM, Piazza dei Cavalieri 7, I-56126 Pisa, Italy 2 Drug Discovery and Development, Italian Institute of Technology, via Morego 30, Genova I-161631, Italy † These authors contributed equally to the work. ‡ Current address: Dipartimento di Fisica, Università di Roma ”La Sapienza”, I-00158 Rome, Italy.
* Author to whom correspondence should be addressed.
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)
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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

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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.

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