Andrzej Kloczkowski

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Two-body inter-residue contact potentials for proteins have often been extracted and extensively used for threading. Here, we have developed a new scheme to derive four-body contact potentials as a way to consider protein interactions in a more cooperative model. We use several datasets of protein native structures to demonstrate that around 500 chains are(More)
BACKGROUND The abundant data available for protein interaction networks have not yet been fully understood. New types of analyses are needed to reveal organizational principles of these networks to investigate the details of functional and regulatory clusters of proteins. RESULTS In the present work, individual clusters identified by an eigenmode analysis(More)
BACKGROUND Protein-protein interactions play a critical role in protein function. Completion of many genomes is being followed rapidly by major efforts to identify interacting protein pairs experimentally in order to decipher the networks of interacting, coordinated-in-action proteins. Identification of protein-protein interaction sites and detection of(More)
SUMMARY We have created the GOR V web server for protein secondary structure prediction. The GOR V algorithm combines information theory, Bayesian statistics and evolutionary information. In its fifth version, the GOR method reached (with the full jack-knife procedure) an accuracy of prediction Q3 of 73.5%. Although GOR V has been among the most successful(More)
The high packing density inside proteins leads to certain geometric regularities and also is one of the most important contributors to the high extent of cooperativity manifested by proteins in their cohesive domain motions. The orientations between neighboring nonbonded residues in proteins substantially follow the similar geometric regularities,(More)
BACKGROUND The ability to generate, visualize, and analyze motions of biomolecules has made a significant impact upon modern biology. Molecular Dynamics has gained substantial use, but remains computationally demanding and difficult to setup for many biologists. Elastic network models (ENMs) are an alternative and have been shown to generate the dominant(More)
Inverse problems are ill-posed: the error function has its minimum in a flat elongated valley or surrounded by many local minima. Local optimization methods give unpredictable results if no prior information is available. Traditionally this has generated mistrust for the use of inverse methods. Stochastic approaches to inverse problems consists in shift(More)
Despite the suitability of various lattice geometries for coarse-grained modeling of proteins, the actual packing geometry of residues in folded structures has remained largely unexplored. A strong tendency to assume a regular packing geometry is shown here by optimally reorienting and superimposing clusters of neighboring residues from databank structures(More)
A new bioinformatics tool for molecular modeling of the local structure around phosphorylation sites in proteins has been developed. Our method is based on a library of short sequence and structure motifs. The basic structural elements to be predicted are local structure segments (LSSs). This enables us to avoid the problem of non-exact local description of(More)
This Provisional PDF corresponds to the article as it appeared upon acceptance. The fully-formatted PDF version will become available shortly after the date of publication, from the URL listed below. Like all articles in BMC journals, this peer-reviewed article was published immediately upon acceptance. It can be downloaded, printed and distributed freely(More)