RepEx: A web server to extract sequence repeats from protein and DNA sequences.

Evolution builds up new genetic material from existing ones, not in random, but in highly ordered and eloquent patterns. Most of these sequence repeats are revelatory of valuable information contributing to areas of disease research and function of macromolecules, to name a few. In the age of next generation genome sequencing, rapid and efficient extraction of all unbiased sequence repeats from macromolecules is the need of the hour.

Glaucoma Pred: Glaucoma prediction based on Myocilin genotype and phenotype information.

Glaucoma is the second leading cause of blindness after cataract and is heterogeneous in nature. Employing a genetic approach for the detection of the diseased condition provides an advantage that the gene responsible for the disease can be identified by genetic test. The availability of predictive tests based on the published literature would provide a mechanism for early detection and treatment.

Opioid Receptor Modulators with a Cinnamyl Group.

To obtain selective and potent opioid receptor ligands, we synthesized dehydro derivatives of alvimopan and found compound (28f), a selective but modest affinity MOR antagonist weaker than alvimopan (1). We replaced the arylpiperidine unit by an arylpiperazine to obtain the 1-(α-carboxycinnamyl)-4-arylpiperazines like 13h, which to our surprise had no MOR or DOR activity but was a KOR agonist with moderate affinity. In contrast, literature examples of arylpiperazines 4 and 5 were reported to be pan opioid receptor antagonists, while 6 was a MOR agonist.

PanGeT: Pan-genomics tool.

A decade after the concept of Pan-genome was first introduced; research in this field has spread its tentacles to areas such as pathogenesis of diseases, bacterial evolutionary studies and drug resistance. Gene content-based differentiation of virulent and a virulent strains of bacteria and identification of pathogen specific genes is imperative to understand their physiology and gain insights into the mechanism of genome evolution. Subsequently, this will aid in identifying diagnostic targets and in developing and selecting vaccines.

Algorithm to find distant repeats in a single protein sequence.

Distant repeats in protein sequence play an important role in various aspects of protein analysis. A keen analysis of the distant repeats would enable to establish a firm relation of the repeats with respect to their function and three-dimensional structure during the evolutionary process. Further, it enlightens the diversity of duplication during the evolution.

Role of water molecules and ion pairs in Dps and related ferritin-like structures.

A comparative study of water molecules and ion pairs in 11 Dps protein structures has been carried out. The invariant and common water molecules, the conserved residues interacting with them and the conserved ion pairs have been analyzed. Certain water molecules found on the interfaces between subunits are highly conserved and may be implicated in flexibility or continuing association of the subunits of the structure.

Ion pairs in non-redundant protein structures.

Ion pairs contribute to several functions including the activity of catalytic triads, fusion of viral membranes, stability in thermophilic proteins and solvent-protein interactions. Furthermore, they have the ability to affect the stability of protein structures and are also a part of the forces that act to hold monomers together. This paper deals with the possible ion pair combinations and networks in 25% and 90% non-redundant protein chains.

SMS: sequence, motif and structure--a database on the structural rigidity of peptide fragments in non-redundant proteins.

Structure prediction methods aim to identify the relationship between the amino acid sequence of an unknown protein and information comprised in databases of known protein structures. Towards this end, we created a database by combining the amino acid sequences and the corresponding three-dimensional atomic coordinates for all the 25% non-redundant protein chains available in the Protein Data Bank. It contains information about the peptide fragments that are 5 to 10 residues long.