Model of protein fragments and statistical potentials

DOI10.1134/S2070046616040051MaRDI QIDQ1702095zbMATH OpenOpenAlexFDO

Authors S. V. Kozyrev

Publication date 27 February 2018

Published in \(p\)-Adic Numbers, Ultrametric Analysis, and Applications (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1504.03940

zbMATH Keywords

hierarchical models of proteinsprotein fragmentsstatistical potentials

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Protein sequences, DNA sequences (92D20)

Abstract: We discuss a model of protein conformations where the conformations are combinations of short fragments from some small set. For these fragments we consider a distribution of frequencies of occurrence of pairs (sequence of amino acids, conformation), averaged over some balls in the spaces of sequences and conformations. These frequencies can be estimated due to smallness of epsilon-entropy of the set of conformations of protein fragments. We consider statistical potentials for protein fragments which describe the mentioned frequencies of occurrence and discuss model of free energy of a protein where the free energy is equal to a sum of statistical potentials of the fragments. We also consider contribution of contacts of fragments to the energy of protein conformation, and contribution from statistical potentials of some hierarchical set of larger protein fragments. This set of fragments is constructed using the distribution of frequencies of occurrence of short fragments. We discuss applications of this model to problem of prediction of the native conformation of a protein from its primary structure and to description of dynamics of a protein. Modification of structural alignment taking into account statistical potentials for protein fragments is considered and application to threading procedure for proteins is discussed.

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Cited in

(9)

• Protein model refinement using structural fragment tessellation
• Statistical formulae of the energy distribution among a globular protein structure ensemble
• The structural modeling of EF-hand motifs in parvalbumin
• Analyzing the sequence-structure relationship of a library of local structural prototypes
• \(p\)-adic mathematical physics: the first 30 years
• On the physical relevance and statistical interpretation of knowledge-based potentials
• Towards a general probabilistic model of protein structure: the reference ratio method
• Using an abstraction of amino acid types to improve the quality of statistical potentials for protein structure prediction
• Sampling conformation space to model equilibrium fluctuations in proteins

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Uses Software

• darch

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