The Protein Data Bank in Europe (PDBe) ( http://www.ebi.ac.uk/pdbe/ ) is actively working
with its Worldwide Protein Data Bank partners to enhance the quality and consistency of the …

Graph theory offers a convenient and highly attractive approach to various tasks of pattern
recognition. Provided there is a graph representation of the object in question (eg a chemical …

The assumption that crystal contacts reflect natural macromolecular interactions makes a
basis for many studies in structural biology. However, the crystal state may correspond to a …

… between residue conservation C and structure similarity scores (Krissinel and Henrick,2004): …
Besides, η B distribution spans from 0.4 to 1 thus populating almost half of all bins. These …

We discuss basic physical–chemical principles underlying the formation of stable
macromolecular complexes, which in many cases are likely to be the biological units performing a …

This paper presents a discussion of existing methods for the analysis of macromolecular
interactions and complexes in crystal packing. Typical situations and conditions where wrong …

… protein chains A and B, of length N A and N B , respectively, are split into sets of overlapping
short fragments of length M, F A / B = { f i A / B } , such that there are L A/B = N A/B − M + 1 …

… (step 3), loop B.2 runs over all interfaces found in {I} and not found in {T}, in steps B.4 and
B.7 the algorithm disengages interface Ik and any interfaces induced by that, steps B.9-…

The paper describes the algorithm of multiple alignment of protein structures in 3D used in
the EBI-MSD web service SSM (Secondary Structure Matching) located at URL given in the …

… may optionally include local servers, running on client machines, for launching locally
installed CCP4 desktop applications such as Coot, CCP4mg or ViewHKL (Evans & Krissinel, …