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1 Bio-Algorithms and Med-Systems

1 2011

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Ab initio protein structure prediction – the hydrophobicity distribution analysis

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Evangelista G. , Minervini G. , Polticelli F. , Malawski M. , Szepieniec T. , Flis Ł. , Prymula K. , Kochańczyk M. , Matczyńska E. , Wiśniowski Z. , Salapa K. , Banach M. , Roterman I.

2011

tom Vol. 7, no. 2

5--12

The three-dimensional structures generated for 20 “never born proteins” (NBP – random amino acid sequence with no significant homology to existing proteins) using two different techniques: ROSETTA (called R in the paper) and “fuzzy oil drop” model (called S in the paper) were compared to estimate the accordance with the assumed model estimating the influence of an external force field on the final structure of the protein. Selected structures are those corresponding to the highest (10 proteins) and lowest (10 proteins) RMS-D values obtained measuring the similarity between the R and S structures. The R structures generated according to an internal force field (the individual inter-molecular interaction) including solvation effects were analyzed using the “fuzzy oil drop” model as target model. The second applied model “fuzzy oil drop” generated structures characterized by an ordered hydrophobic core structure. 13 of the 20 selected S structures appeared to be accordant with the “fuzzy oil drop” model while 6 out of the 20 structures appeared to be accordant with external force field for R structures which suggests a general interpretation of the influence of an external force field on the folding simulation.