The growing number of large macromolecular complexes in the Protein Data Bank (PDB) has warranted a closer look at these structures. An overview of the types of molecules that form these large complexes is presented here. Some of the challenges at the PDB in representing, archiving, visualizing, and analyzing these structures are discussed along with possible means to overcome them.

Proteins of uncharacterized functions form a large part of many of the currently available biological databases and this situation exists even in the Protein Data Bank (PDB). Our analysis of recent PDB data revealed that only 42.53% of PDB entries (1084 coordinate files) that were categorized under "unknown function" are true examples of proteins of unknown function at this point in time. The r...

The wwPDB responds to the article On the prompt update of literature references in the Protein Data Bank [Wlodawer (2014), Acta Cryst. D70, 2779].

Protein structures come in families. Are families "closely knit" or "loosely knit" entities? We describe a measure of relatedness among polymer conformations. Based on weighted distance maps, this measure differs from existing measures mainly in two respects: (1) it is computationally fast, and (2) it can compare any two proteins, regardless of their relative chain lengths or degree of similari...

In his 1997 paper on solving Rubik’s Cube optimally using IDA* and pattern database heuristics (PDBs), Rich Korf conjectured that there was an inverse relationship between the size of a PDB and the amount of time required for IDA* to solve a problem instance on average. In the current paper, I examine the implications of this relationship, in particular how it limits the ability of abstraction-...

Updating literature references in the Protein Data Bank is discussed.

Admissible heuristics are critical for effective domainindependent planning when optimal solutions must be guaranteed. Two useful heuristics are the h heuristics, which generalize the reachability heuristic underlying the planning graph, and pattern database heuristics. These heuristics, however, have serious limitations: reachability heuristics capture only the cost of critical paths in a rela...

Up to 2% of X-ray structures in the Protein Data Bank (PDB) potentially fit into a higher symmetry space group. Redundant protein chains in these structures can be made compatible with exact crystallographic symmetry with minimal atomic movements that are smaller than the expected range of coordinate uncertainty. The incidence of problem cases is somewhat difficult to define precisely, as there...

The properties of 1172 protein complexes (downloaded from the Protein Data Bank (PDB)) have been studied based on the concept of circular variance as a buriedness indicator and the concept of mutual proximity as a parameter-free definition of contact. The propensities of residues to be in the protein, on the surface or form contact, as well as residue pairs to form contact were calculated. In a...

performance evaluation has been developed in the form of management schools along by managerial thought development. banks and financial institutes are one of the most important economic sections to each country which by receipts and payments directing and organizing facilitate business and commercial transactions and develop markets and economic growth and as the main pillars in directing and ...