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2 Bio-Algorithms and Med-Systems

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RandomBlast a tool to generate random “never born protein” sequences

100%

Evangelista G. , Minervini G. , Luisi P. L. , Polticelli F.

Bio-Algorithms and Med-Systems

2007

tom Vol. 3, no. 5

27--31

In an accompanying paper by Minervini et al., we deal with the scientific problem of studying the sequence to structure relationships in “never born proteins” (NBPs), i.e. protein sequences which have never been observed in nature. The study of the structural and functional properties of "never born proteins" requires the generation of a large library of protein sequences characterized by the absence of any significant similarity with all the known protein sequences. In this paper we describe the implementation of a simple command-line software utility used to generate random amino acid sequences and to filter them against the NCBI non redundant protein database, using as a threshold the value of the Evalue parameter returned by the well known sequence comparison software Blast. This utility, named RandomBlast, has been written using C programming language for Windows operating systems. The structural implications of NBPs random amino acid composition are discussed as compared to natural proteins of comparable length.

Ab initio protein structure prediction – the hydrophobicity distribution analysis

51%

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.