this paper considers the generation of some interpretable fuzzy rules for assigning an amino acid sequence into the appropriate protein superfamily. since the main objective of this classifier is the interpretability of rules, we have used the distribution of amino acids in the sequences of proteins as features. these features are the occurrence probabilities of six exchange groups in the seque...

ProClass is a protein family database that organizes non-redundant sequence entries into families defined collectively by PROSITE patterns and PIR superfamilies. By combining global similarities and functional motifs into a single classification scheme, ProClass helps to reveal domain and family relationships and classify multi-domain proteins. The database currently consists of more than 120 0...

The validation, enrichment and organization of the data stored in PDB files is essential for those data to be used accurately and efficiently for modelling, experimental design and the determination of molecular interactions. The Iditis protein structure database has been designed to allow the widest possible range of queries to be performed across all available protein structures. The Iditis d...

Halophilic archaea/bacteria adapt to different salt concentration, namely extreme, moderate and low. These type of adaptations may occur as a result of modification of protein structure and other changes in different cell organelles. Thus proteins may play an important role in the adaptation of halophilic archaea/bacteria to saline conditions. The Halophile protein database (HProtDB) is a syste...

The fluorescence properties of tryptophan residues are sensitive to the microenvironment of tryptophan fluorophores in proteins. Therefore, fluorescence characteristics are widely used to study structural transitions in proteins. We have developed algorithms for the decomposition of multi-component protein fluorescence spectra and the correlation of these spectral parameters with protein struct...

Following the completion of full genome sequences for several model organisms, protein interaction networks of some viral, prokaryotic and eukaryotic species have been established gradually. Many studies have already elucidated that the functional related proteins of different species were regulated in similar mechanism. In last decade, most of the protein interactions existed in yeast (S. cere...

Protein S-palmitoylation is a reversible post-translational modification that regulates many key biological processes, although the full extent and functions of protein S-palmitoylation remain largely unexplored. Recent developments of new chemical methods have allowed the establishment of palmitoyl-proteomes of a variety of cell lines and tissues from different species.  As the amount of infor...