Markov entropy backbone electrostatic descriptors for predicting proteins biological activity.
Bioorg Med Chem Lett
; 14(18): 4691-5, 2004 Sep 20.
Article
em En
| MEDLINE
| ID: mdl-15324889
ABSTRACT
The spherical truncation of electrostatic interactions between aminoacids makes it possible to break down long-range spatial electrostatic interactions, resulting in short-range interactions. As a result, a Markov Chain model may be used to calculate the probabilities with which the effect of a given interaction reaches aminoacids at different distances within the backbone. The entropies of a Markov Chain model of this type may then be used to codify information about the spatial distribution of charges in the protein used in this study exploring the structure-activity relationship. In this paper, a linear discriminant analysis is reported, which correctly classified 92.3% of 26 under investigation in training and leave-one-out cross validation, purely for illustrative purposes. Classification was carried out for three possible activities lysozymes, dihydrofolate reductases, and alcohol dehydrogenases. The discriminant analysis equations were contracted into two canonical roots. These simple canonical roots have high regression coefficients (R(c1)=0.903 and R(c2)=0.70). Root1 explains the biological activity of alcohol dehydrogenases while Root2 discriminates between lysozymes and dihydrofolate reductases. It was possible to profile the effect of core, middle, and surface aminoacids on biological activity. In contrast, a model considering classic physicochemical parameters such as polarizability, refractivity, and partition coefficient classify correctly only the 80.8% of the proteins.
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Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Proteínas
/
Cadeias de Markov
Tipo de estudo:
Health_economic_evaluation
/
Prognostic_studies
/
Risk_factors_studies
Idioma:
En
Revista:
Bioorg Med Chem Lett
Assunto da revista:
BIOQUIMICA
/
QUIMICA
Ano de publicação:
2004
Tipo de documento:
Article
País de afiliação:
Cuba