Toward a unified scoring function for native state discrimination and drug-binding pocket recognition
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By shifting the balance between conformational entropy and internal energy, polymers modify their shape under external stimuli, such as changes in temperature. Prominent among such transformations is the coil-globule transition, whereby a polymer can switc ...
Molecular dynamics (MD) simulations have increasingly contributed to the understanding of biomolecular processes, allowing for predictions of thermodynamic and structural properties. Unfortunately, the holy grail of protein structure prediction was soon fo ...
The conformational search for favorable intramolecular interactions during protein folding is limited by intrachain diffusion processes. Recent studies on the dynamics of loop formation in unfolded polypeptide chains have focused on loops involving residue ...
Limited searching in the conformational space is one of the major obstacles for investigating protein dynamics by numerical approaches. For this reason, classical all-atom mol. dynamics (MD) simulations of proteins tend to be confined to local energy min., ...
Characteristic timescales associated with the function of biomolecules, like proteins, range from femtoseconds up to minutes, whereas their corresponding spatial extent ranges from few ̊A to μm when associating in large macromolecular complexes. Moreover, ...
To find out whether the AGO-miRNA complex is more sensitive to the accessibility of a particular region inside the seed match, we analyze in detail the accessibility of a wide set of miRNA binding sites validated by PAR-CLIP and HITS-CLIP experiments. Our ...
Cold Spring Harbor Lab Press, Publications Dept2012
Indoleamine 2,3-dioxygenase 1 (IDO1) is an important therapeutic target treatment of diseases such as cancer that involve pathological immune escape. Starting from the scaffold of our previously discovered IDO1 inhibitor 4-phenyl-1,2,3-triazole, we used co ...
A misfolded conformer of the cellular prion protein, denoted as scrapie prion protein, is considered responsible for a variety of fatal neurodegenerative diseases. Both, the function of the protein in its native conformation as well as the factors that tri ...
Intrachain loop formation allows unfolded polypeptide chains to search for favorable interactions during protein folding. We applied triplet-triplet energy transfer between a xanthone moiety and naphthylalanine to directly measure loop formation in various ...
The specific labeling of proteins with synthetic probes is a powerful approach to study protein function and protein tags have been widely used for this purpose. A well-established example for a self-labeling protein tag is SNAP-tag. It specifically reacts ...
