Many proteins undergo changes in their structure during biochemical processes such as binding and transport. Such conformational changes are crucial to the functioning of proteins, and by extension, to most biological processes. This thesis describes algorithms for detecting conformational changes from protein structure data. Conformational changes may be determined by comparing protein structu...

The PDBSite database provides comprehensive structural and functional information on various protein sites (post-translational modification, catalytic active, organic and inorganic ligand binding, protein-protein, protein-DNA and protein-RNA interactions) in the Protein Data Bank (PDB). The PDBSite is available online at http://wwwmgs.bionet.nsc.ru/mgs/gnw/pdbsite/. It consists of functional si...

UNLABELLED Cage-shaped protein, with its special structure, may have potential applications in biomedicine and nanotechnology. We developed a program CSPro (Cage-Shaped Protein) for efficient identification of cage-shaped proteins based on quaternary structure. CSPro is capable of revealing the corresponding cage-shaped feature more clearly and quickly than traditional visualization tools. Usin...

UNLABELLED sGAL is a computer program designed to find pairs of sites suitable for introducing chemical cross-links into proteins. sGAL takes a protein structure file in PDB format as input, truncates each residue sequentially to its gamma side chain atom to mimic mutation to Cys, and calculates the exposed surface area of the gamma atom. The user then inputs the minimum and maximum lengths of ...

Summary: We have created a new server FoldHandedness. Using this server it is possible: (i) to define the regions of helices from two issues (from the PDB file and using the last version of the DSSP program), (ii) to determine the handedness for any chosen three helices and (iii) to calculate the angle and sign between the chosen pairs of the helices for large proteins and complexes of proteins...

A statistical analysis of the PDB structures has led us to define a new set of small 3D structural prototypes called Protein Blocks (PBs). This structural alphabet includes 16 PBs, each one is defined by the (phi, psi) dihedral angles of 5 consecutive residues. The amino acid distributions observed in sequence windows encompassing these PBs are used to predict by a Bayesian approach the local 3...

banks are one of the most important financial sectors in order to the economic development of each country. certainly, efficiency scores and ranks of banks are significant and effective aspects towards future planning. sometimes the performance of banks must be measured in the presence of undesirable and vague factors. for these reasons in the current paper a procedure based on data envelopment...

Information on the preparation and characterization of heavy-atom derivatives of protein crystals has been collected, either from the literature or directly from protein crystallographers, and assembled in the form of a heavy-atom data bank (HAD). The data bank contains coordinate data for the heavy-atom positions in a form that is compatible with the crystallographic data in the Brookhaven Pro...

This Briefing reviews the widely used, currently active, up-to-date databases derived from the worldwide Protein Data Bank (PDB) to facilitate browsing, finding and exploring its entries. These databases contain visualization and analysis tools tailored to specific kinds of molecules and interactions, often including also complex metrics precomputed by experts or external programs, and connecti...