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Association and dissociation of protein molecules are crucial for most of the cellular processes. A protein-protein interface (PPI) is defined by a pair of regions of two interacting protein molecules that are linked by non-covalent bonds. Analysis and classification of PPIs may help to recognize certain interface binding organizations shared by different protein families, which may be importan...
MOTIVATION The discovery of motifs in biosequences is frequently torn between the rigidity of the model on the one hand and the abundance of candidates on the other. In particular, the variety of motifs described by strings that include 'don't care' (dot) patterns escalates exponentially with the length of the motif, and this gets only worse if a dot is allowed to stretch up to some prescribed ...
STING Millennium Suite (SMS) is a new web-based suite of programs and databases providing visualization and a complex analysis of molecular sequence and structure for the data deposited at the Protein Data Bank (PDB). SMS operates with a collection of both publicly available data (PDB, HSSP, Prosite) and its own data (contacts, interface contacts, surface accessibility). Biologists find SMS use...
We have proposed that the prediction of protein subcellular localization sites can provide a good clue for the characterization of open reading frames of unknown function [1, 2]. Our program, PSORT, has been used by a number of researchers through the Internet [3]. PSORT was originally written in the style of a 'if-then' rule-based system. Although this style has the merit of a great versatilit...
G-protein coupled receptors (GPCRs) constitute a broad class of cell-surface receptors, including several functionally distinct families, that play a key role in cellular signalling and regulation of basic physiological processes. GPCRs are the focus of a significant amount of current pharmaceutical research since they interact with more than 50% of prescription drugs, whereas they still compri...
The function of a protein is generally related to its subcellular localization. Therefore, knowing its subcellular localization is helpful in understanding its potential functions and roles in biological processes. This work develops a hybrid method for computationally predicting the subcellular localization of eukaryotic protein. The method is called EuLoc and incorporates the Hidden Markov Mo...
In this work is presented an approach for the construction of common patterns of the protein motifs of the amyloid protein motifs, extracted from the database AMYPdb, denoted as regular expressions using the rules PROSITE. Our task is to analyze a set of possible motifs and to detect if similarity exists between them, in order to construct a general motif. The Ant Colony Optimization Model uses...
The ExPASy (the Expert Protein Analysis System) World Wide Web server (http://www.expasy.org), is provided as a service to the life science community by a multidisciplinary team at the Swiss Institute of Bioinformatics (SIB). It provides access to a variety of databases and analytical tools dedicated to proteins and proteomics. ExPASy databases include SWISS-PROT and TrEMBL, SWISS-2DPAGE, PROSI...
We have performed a comprehensive analysis of the microenvironments surrounding the twenty amino acids. Our analysis includes comparison of amino acid environments with random control environments as well as with each of the other amino acid environments. We describe the amino acid environments with a set of 21 features summarizing atomic, chemical group, residue, and secondary structural featu...
In this series of projects of sequencing human cDNA clones which correspond to relatively long and nearly full-length transcripts, we newly determined the sequences of 80 clones, and predicted the coding sequences of the corresponding genes, named KIAA0201 to KIAA0280. Among the sequenced clones, 68 were obtained from human immature myeloid cell line KG-1 and 12 from human brain. The average si...
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