Protein structure predictions, and experimentally derived protein structures, very often
require certain structure improvement (refinement), which means bringing it closer to real …

The understanding of the folding mechanisms of single-domain proteins is an essential step
in the understanding of protein folding in general. Recently, we developed a mesoscopic CA …

To predict the tertiary structure of full‐length sequences of all targets in CASP6, regardless
of their potential category (from easy comparative modeling to fold recognition to apparent …

In this Note we present a new software library for structural bioinformatics. The library
contains programs, computing sequence-and profile-based alignments and a variety of …

Abstract Cytochrome P450 monooxygenases (CYPs/P450s) are heme‐containing enzymes
known to biology for more than six decades. Their stereo‐and regio‐specific enzymatic …

BioShell is a suite of programs performing common tasks accompanying protein structure
modeling. BioShell design is based on UNIX shell flexibility and should be used as its …

Background Although experimental methods for determining protein structure are providing
high resolution structures, they cannot keep the pace at which amino acid sequences are …

Background The majority of experimentally determined crystal structures of Type II restriction
endonucleases (REases) exhibit a common PD-(D/E) XK fold. Crystal structures have been …

Atomic-level molecular dynamics simulations are widely used for the characterization of the
structural dynamics of proteins; however, they are limited to shorter time scales than the …

It is well recognized that thermal motions of atoms in the protein native state, the fluctuations
about the minimum of the global free energy, are well reproduced by the simple elastic …