SCit is a web server providing services for protein side chain conformation analysis and side chain positioning. Specific services use the dependence of the side chain conformations on the local backbone conformation, which is described using a structural alphabet that describes the conformation of fragments of four-residue length in a limited library of structural prototypes. Based on this con...

MOTIVATION Characterization of the restricted nature of the protein local conformational space has remained a challenge, thereby necessitating a computationally expensive conformational search in protein modeling. Moreover, owing to the lack of unilateral structural descriptors, conventional data mining techniques, such as clustering and classification, have not been applied in protein structur...

DNA repair enzymes are essential for maintaining the integrity of the DNA sequence. Unfortunately, very little is known about how these enzymes recognize damaged regions along the helix. Structural analysis of cellular repair enzymes bound to DNA reveals that these enzymes are able to recognize DNA in a variety of conformations. However, the prevalence of these deformations in the absence of en...

Two-dimensional 1H-15N HMBC NMR spectra of the well-known anticonvulsant carbamazepine dissolved in different organic solvents, recorded on an spectrometer prove existence hidden conformers saturated solutions. Obtained conformer distribution arises due to presence solid phase solution. A weak influence ring currents was revealed for molecular conformations a solution, which provides simple app...

Molecular dynamics (MD) simulation is a well-established method for understanding protein dynamics. Conformations from unrestrained MD simulations have yet to be assessed for blind virtual screening (VS) by docking. This study presents a critical analysis of the predictive power of MD snapshots to this regard, evaluating two well-characterized systems of varying flexibility in ligand-bound and ...

In this paper we propose a robotics-inspired method to enhance sampling of native-like conformations when employing only aminoacid sequence information for a protein at hand. Computing such conformations, essential to associating structural and functional information with gene sequences, is challenging due to the highdimensionality and the rugged energy surface of the protein conformational spa...

The coarse graining method to be advocated in this paper consists of two main steps. First, the propagation of an ensemble of molecular states is described as a Markov chain by a transition probability matrix in a finite state space. Second, we obtain metastable conformations by an aggregation of variables via Robust Perron Cluster Analysis (PCCA+). Up to now, it has been an open question as to...

DNA origami (DO) nanotechnology has strong potential for applications including molecular sensing, drug delivery, and nanorobotics that rely on nanoscale structural precision the ability to tune mechanical dynamic properties. Given these emerging applications, there is a need broaden access training DO concepts, which would also provide an avenue demonstrate engineering concepts such as kinemat...

Multiple crystal structures of the homo-trimeric protein disulphide isomerase PmScsC reveal that peptide which links trimerization stalk and catalytic domain can adopt helical, β-strand loop conformations. This region has been called a ‘shape-shifter’ peptide. Characterisation this using NMR experiments MD simulations shown it is essentially disordered in solution. Analysis identifies role inte...