ELM: the status of the 2010 eukaryotic linear motif resource.

Linear motifs are short segments of multidomain proteins that provide regulatory functions independently of protein tertiary structure. Much of intracellular signalling passes through protein modifications at linear motifs. Many thousands of linear motif instances, most notably phosphorylation sites, have now been reported.

Analysis of structure and function of tenascin-C.

Tenascin-C is a multidomain large extracellular matrix glycoprotein composed of six monomers. The size of tenascin-C monomers (180-250 kDa) varies as a result of an alternative splicing of the fibronectin repeats at the pre-mRNA level. For the first time we applied bioinformatic and molecular modeling procedures, for detailed analysis of the organization of tenascin-C and we performed bioinformatic analysis of tenascin-C gene.

Lead toxicity through the leadzyme.

Lead is one of the most dangerous toxic agents for all living organisms. In humans, elevated levels of lead have been linked to a number of disorders for which various molecular mechanisms have been proposed. However, none of them has been fully understood.

Ligand.Info small-molecule Meta-Database.

Ligand.Info is a compilation of various publicly available databases of small molecules. The total size of the Meta-Database is over 1 million entries.

Structure prediction, evolution and ligand interaction of CHASE domain.

Cytokinins are plant hormones involved in the essential processes of plant growth and development. They bind with receptors known as CRE1/WOL/AHK4, AHK2, and AHK3, which possess histidine kinase activity. Recently, the sensor domain cyclases/histidine kinases associated sensory extracellular (CHASE) was identified in those proteins but little is known about its structure and interaction with ligands.

3D-Hit: fast structural comparison of proteins.

3D-Hit is a fast scanning method for detecting structural similarities between proteins. The algorithm is based on a hashing function, which decomposes proteins into segments of 13 residues. The scanning procedures start with assigning a set of similar segments from the database to each segment in the query protein.

Comparison of proteins based on segments structural similarity.

We present here a simple method for fast and accurate comparison of proteins using their structures. The algorithm is based on structural alignment of segments of Calpha chains (with size of 99 or 199 residues). The method is optimized in terms of speed and accuracy.

The PDB-Preview database: a repository of in-silico models of 'on-hold' PDB entries.

Unlabelled: The PDB-Preview database is a dynamic web repository of in-silico predicted three-dimensional (3D) models of experimentally determined structures that are deposited into the PDB but are not yet publicly released, and are kept 'on-hold'. The PDB-Preview database is automatically generated on a weekly basis by the bioinfo.pl meta-server, which uses top-of-the-line fold-recognition methods.

Two sequences encoding chalcone synthase in yellow lupin (Lupinus luteus l.) may have evolved by gene duplication.

Two full copy cDNA sequences encoding chalcone synthase (CHS) were selected from a yellow lupin (Lupinus luteus L.) root and nodule cDNA library, and sequenced. Analysis of their open reading frames gave evidence that both encode the functional enzyme.

Application of 3D-Jury, GRDB, and Verify3D in fold recognition.

In CASP5, the BioInfo.PL group has used the structure prediction Meta Server and the associated newly developed flexible meta-predictor, called 3D-Jury, as the main structure prediction tools. The most important feature of the meta-predictor is a high (86%) correlation between the reported confidence score and the quality of the selected model.

ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure.

ORFeus is a fully automated, sensitive protein sequence similarity search server available to the academic community via the Structure Prediction Meta Server (http://BioInfo.PL/Meta/). The goal of the development of ORFeus was to increase the sensitivity of the detection of distantly related protein families.

Ligand-Info, searching for similar small compounds using index profiles.

Motivation: The Ligand-Info system is based on the assumption that small molecules with similar structure have similar functional (binding) properties. The developed system enables a fast and sensitive index based search for similar compounds in large databases. Index profiles, constructed by averaging indexes of related molecules are used to increase the specificity of the search.

Molecular phylogenetics of the RrmJ/fibrillarin superfamily of ribose 2'-O-methyltransferases.

Recent analyses identified a putative catalytic tetrad K-D-K-E common to several families of site-specific methyltransferases (MTases) that modify 2'-hydroxyl groups of ribose in mRNA, rRNA and tRNA (designated the RrmJ class after one of the structurally characterized members; 1eiz in Protein Data Bank) [Genome Biol. 2(9) (2001) 38]. Subsequently, three residues of the tetrad (K-D-K) were shown to be essential for catalysis in RrmJ [J.