An intuitive graphical webserver for multiple-choice protein sequence search.

Every day tens of thousands of sequence searches and sequence alignment queries are submitted to webservers. The capitalized word "BLAST" becomes a verb, describing the act of performing sequence search and alignment. However, if one needs to search for sequences that contain, for example, two hydrophobic and three polar residues at five given positions, the query formation on the most frequently used webservers will be difficult.

AmphoraNet: the webserver implementation of the AMPHORA2 metagenomic workflow suite.

Motivation: Metagenomics went through an astonishing development in the past few years. Today not only gene sequencing experts, but numerous laboratories of other specializations need to analyze DNA sequences gained from clinical or environmental samples. Phylogenetic analysis of the metagenomic data presents significant challenges for the biologist and the bioinformatician.

Equal opportunity for low-degree network nodes: a PageRank-based method for protein target identification in metabolic graphs.

Biological network data, such as metabolic-, signaling- or physical interaction graphs of proteins are increasingly available in public repositories for important species. Tools for the quantitative analysis of these networks are being developed today. Protein network-based drug target identification methods usually return protein hubs with large degrees in the networks as potentially important targets.

3-d brownian motion simulator for high-sensitivity nanobiotechnological applications.

A wide variety of nanobiotechnologic applications are being developed for nanoparticle based in vitro diagnostic and imaging systems. Some of these systems make possible highly sensitive detection of molecular biomarkers. Frequently, the very low concentration of the biomarkers makes impossible the classical, partial differential equation-based mathematical simulation of the motion of the nanoparticles involved.

NASCENT: an automatic protein interaction network generation tool for non-model organisms.

Unlabelled: Large quantity of reliable protein interaction data are available for model organisms in public depositories (e.g., MINT, DIP, HPRD, INTERACT).