Protein 3D structure is one of the key factors in recognizing gene functions. The availability of protein structure data in Protein Data Bank (PDB) enables us to conduct gene function analysis. However, the molecules in the PDB, whose structures have been determined, are always not corresponding to a unique gene. That is to say, the mapping from gene to PDB is not one-to-one. Thus this uncertai...

Models based on the crystal structure of interleukin-1 vary significantly. D eP ri st o/ El se vi er UK) warns that, for any given structure in the Protein Data Bank (PDB), there will be many other overlooked structures that are equally consistent with the data. Crystallized proteins retain the ability to move around, thus making interpretations of diffraction data an imprecise process. Crystal...

Models based on the crystal structure of interleukin-1 vary significantly. D eP ri st o/ El se vi er UK) warns that, for any given structure in the Protein Data Bank (PDB), there will be many other overlooked structures that are equally consistent with the data. Crystallized proteins retain the ability to move around, thus making interpretations of diffraction data an imprecise process. Crystal...

Models based on the crystal structure of interleukin-1 vary significantly. D eP ri st o/ El se vi er UK) warns that, for any given structure in the Protein Data Bank (PDB), there will be many other overlooked structures that are equally consistent with the data. Crystallized proteins retain the ability to move around, thus making interpretations of diffraction data an imprecise process. Crystal...

MOTIVATION The Protein Data Bank (PDB) contains over 43,800 experimentally determined 3D models of macromolecular structures and their complexes. Each 3D model reveals something interesting and important about the given molecule's function and biological significance. Usually the best source of this information is the original article describing it, and it is often possible to discern the key a...

R3D-BLAST is a BLAST-like search tool that allows the user to quickly and accurately search against the PDB for RNA structures sharing similar substructures with a specified query RNA structure. The basic idea behind R3D-BLAST is that all the RNA 3D structures deposited in the PDB are first encoded as 1D structural sequences using a structural alphabet of 23 distinct nucleotide conformations, a...

The Protein Data Bank (PDB) is one of the richest sources of structural biological information in the World. It started to exist as the computer-readable depository of crystallographic data complementing printed papers. The proper interpretation of the content of the individual files in the PDB still needs the detailed information found in the citing publication. An advanced graph theoretical m...

A comprehensive database named, protein ligand interaction database (PLID), is created with 6295 ligands bound to proteins extracted from the protein data bank (PDB). This is by far the most comprehensive database of physico-chemical properties, quantum mechanical descriptors and the residues present in the active site of proteins. It is a publicly available web-based database (via the Internet...

We developed a database called RNAJunction that contains structure and sequence information for RNA structural elements such as helical junctions, internal loops, bulges and loop-loop interactions. Our database provides a user-friendly way of searching structural elements by PDB code, structural classification, sequence, keyword or inter-helix angles. In addition, the structural data was subjec...

Structural genomics initiatives have started to accumulate protein structures of unknown function in an increasing pace. Conventional sequence-based function prediction methods are not able to provide useful function information to most of such structures. Thus, structure-based approaches have been developed, which predict function of proteins by capturing structural characteristics of function...