| Markov entropy backbone electrostatic descriptors for predicting proteins biological activity. | |
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MedLine Citation:
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PMID: 15324889 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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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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Authors:
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Humberto González-Díaz; Reinaldo Molina; Eugenio Uriarte |
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Publication Detail:
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Type: Comparative Study; Journal Article; Research Support, Non-U.S. Gov't |
Journal Detail:
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Title: Bioorganic & medicinal chemistry letters Volume: 14 ISSN: 0960-894X ISO Abbreviation: Bioorg. Med. Chem. Lett. Publication Date: 2004 Sep |
Date Detail:
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Created Date: 2004-08-24 Completed Date: 2005-03-07 Revised Date: 2008-11-21 |
Medline Journal Info:
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Nlm Unique ID: 9107377 Medline TA: Bioorg Med Chem Lett Country: England |
Other Details:
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Languages: eng Pagination: 4691-5 Citation Subset: IM |
Affiliation:
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Chemical Bioactives Center, Central University of 'Las Villas' 54830, Cuba. humbertogd@vodafone.es |
Export Citation:
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APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
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Alcohol Dehydrogenase
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chemistry,
pharmacology Linear Models Markov Chains* Muramidase / chemistry, pharmacology Probability Proteins / chemistry*, pharmacology* Quantitative Structure-Activity Relationship Static Electricity Tetrahydrofolate Dehydrogenase / chemistry, pharmacology |
| Chemical | |
Reg. No./Substance:
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0/Proteins; EC 1.1.1.1/Alcohol Dehydrogenase; EC 1.5.1.3/Tetrahydrofolate Dehydrogenase; EC 3.2.1.17/Muramidase |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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