Krzysztof A. Olszewski

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Proposed is a method for locating functionally relevant atoms in protein structures and a representation of spatial arrangements of these atoms allowing for a flexible description of active sites in proteins. The search method is based on comparison of local structure features of proteins that share a common biochemical function. The method does not depend(More)
To maximise the assignment of function of the proteins encoded by a genome and to aid the search for novel drug targets, there is an emerging need for sensitive methods of predicting protein function on a genome-wide basis. GeneAtlas is an automated, high-throughput pipeline for the prediction of protein structure and function using sequence similarity(More)
Amino acid sequences of native proteins are generally not palindromic. Nevertheless, the protein molecule obtained as a result of reading the sequence backwards, i.e. a retro-protein, obviously has the same amino acid composition and the same hydrophobicity profile as the native sequence. The important questions which arise in the context of retro-proteins(More)
In solution, the B domain of protein A from Staphylococcus aureus (B domain) possesses a three-helix bundle structure. This simple motif has been previously reproduced by Kolinski and Skolnick (Proteins 18: 353-366, 1994) using a reduced representation lattice model of proteins with a statistical interaction scheme. In this paper, an improved version of the(More)
An analysis of different approaches to protein structure prediction is presented based solely on the range of models submitted to the third Critical Assessment of Protein Structure Prediction (CASP3) conference. CASP conferences evaluate the current state of the art of protein structure prediction by comparing blind prediction efforts of many groups for the(More)
A choice of sequence-structure similarity scoring function parameters can significantly alter results of the performance of the recognition of distantly related folds. It therefore constitutes a critical part of fold recognition process. In order to increase an understanding of the influence of parameter choice, a comprehensive benchmark of very hard(More)
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