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1

Przewidywanie struktury drugorzędowej białek metodą słownikową

Fabian P., Stąpor K.

Studia Informatica

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2014

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Vol. 35, nr 1

57--68

EN

This paper describes a method of predicting the secondary structure of proteins, based on dictionaries of subsequences. These subsequences are derived from records available in the PDB database. Depending on the construction of the learning set, accuracies of up to 79% have been achieved. Dictionaries use hashing functions, which make them fast and capable of storing large sets of substrings.

PL

W artykule opisano sposób przewidywania struktury drugorzędowej białek, oparty na słownikach podciągów. Sekwencje te są pobierane z danych dostępnych w bazie danych PDB. W zależności od konstrukcji zestawu uczącego, osiągnięto dokładność do 79%. Do szybkiego dostępu do słowników zawierających dużą liczbę podciągów zastosowano funkcje mieszające.

2

Examples of new models applied in selected simulation systems with respect to database

Ignaszak Z., Hajkowski J., Popielarski P.

Archives of Foundry Engineering

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2013

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Vol. 13, iss. 1

45--50

EN

The tolerance of damage rule progressively meets the approval in the design casting parts procedures. Therefore, there were appeared the new challenges and expectations for permanent development of process virtualization in the mechanical engineering industry. Virtualization is increasingly developed on the stage of product design and materials technologies optimization. Increasing expectations of design and process engineers regarding the practical effectiveness of applied simulation systems with new proposed up-grades modules is observed. The purpose is to obtain simulation tools allowing the most possible realistic prognosis of the casting structure, including indication, with the highest possible probability, places in the casting that are endangered with the possibility of shrinkage– and gas porosity formation. This 3D map of discontinuities and structure transformed in local mechanical characteristics are used to calculate the local stresses and safety factors. The needs of tolerance of damage and new approach to evaluate the quality of such prognosis must be defined. These problems of validation of new models/modules used to predict the shrinkage– and gas porosity including the chosen structure parameters in the example of AlSi7 alloy are discussed in the paper.

3

SSTMProt, a point mutation sensitive tool to combine results and to predict the consensus sequence, and secondary structure of transmembrane proteins

Jastrzębski J. P.

Bio-Algorithms and Med-Systems

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2011

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Vol. 7, no. 4

67--78

EN

The efficiency of predictions of protein secondary structures can be increased by treating this process as a cycle of steps, where each step is an approach to the single natural event in folding process (model and simulation of successive events). The set of simulation steps qualifies reliability of in silico simulation of single steps, allowing to verify the correctness of each step as well as to retain sensitivity in case of a single amino acidic substitution. For this purpose the three-part algorithm (SSTMProt) has been designed. This algorithm combines the results of known methods of prediction of proteins secondary structure. Furthermore, the efficiency of this algorithm has been verified using the models received from the RCSB PDB (the Research Collaboratory for Structural Bioinformatics – Protein Data Base; http://www.rcsb.org). The accuracy of known methods has been compared with the accuracy of designed algorithms. The accuracy has been tested by the comparison of true secondary structure with predicted secondary structure of a given protein. The results of accuracy test has been presented as percentage values of similarity between both secondary structures: predicted structure using known method vs. true structure and predicted structure using designed method vs. true structure. The results demonstrate 20-30% higher accuracy of prediction for designed algorithms then for adequate known methods. The test of sensitivity has been done for proteins of a very conservative and stable structure (subunits of bovine cytochrome c oxidase and bacterial ATP-ase, bovine rhodopsin and human hemoblobin as a globular but alpha-helical protein). The influence of a single amino acid substitution on a resulted secondary structure predicted by SSTMProt algorithms has been examined. The repeatability of elaborated algorithms is 100% and each of all 12 tested combinations of methods were sensitive on a single amino acid substitution. All tests have been done for 10 models of native forms of proteins of known structure (models downloaded from the RCSB PDB 1HBB, 1HBS, 1OCC, 1U17, 1C17) and over 500 modified models; 30 known methods of prediction of secondary structure of proteins and 40 combinations of these methods included in three versions of elaborated algorithms have been examined for each protein model.

4

Limitation of conformational space for proteins -- early stage folding simulation of human alpha and beta hemoglobin chains

Bryliński M., Jurkowski W., Konieczny L., Roterman I.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

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2004

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Vol. 8, No 3

413-422

EN

The starting structure of ab initio protein structure prediction methods is problematic as the energy minimization procedure stops searching for an optimal structure of the function's local minimum. The method presented in the paper helps to find the starting structure. Although it is based on the known native protein structure, it seems to deliver a key to the formation of a common universal starting structure. The limited conformational sub-space, defined on the basis of a geometrical model of the polypeptide backbone with the side chain-side chain interaction excluded, seems to deliver the original structure of the polypeptide, which is modified step by step as the role of the side chain interactions increases during the energy minimization procedure. Here, the method is applied to human hemoglobin chains alpha and ß to test the applicability of the method to proteins with a high content of helical forms and lacking disulphide bonds.