Interresidue contacts in protein structures and protein complexes

kavin submitted, created time 7 months 2 weeks (www.ncbi.nlm.nih.gov)

The investigation is extended to a set of protein-protein complexes, showing that the similar global rules apply as for intraprotein contacts, with 64% of the interprotein contacts best described by local structures. The authors then present an evaluation of pairing functions integrating structural letters to decoy scoring and show that some complexes could benefit from the use of structural letter-based pairing functions. Proteins 2008. (c) 2008 Wiley-Liss, Inc.

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It’s All About Geometry: Protein Contact Surfaces Hold Key to Cures

jane2007 submitted, created time 11 months 4 days (ucsdnews.ucsd.edu)

For scientists seeking new treatments for diseases like Parkinson’s and Alzheimer’s, geometry is very important. In the atomic-level landscape of proteins, shape determines the all-important function of these molecules of life.

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Decoding protein structures helps illuminate cause of diabetes

athena submitted, created time 1 year 7 months (www.biologynews.net)

"Any photographer can vouch for the difficulty of capturing a clear picture of a moving target.

When it comes to molecules, however, sometimes the motion is exactly what scientists want to see - for example, to understand the pathological protein mis-folding and assembly that seem to underlie a host of human disorders, including diabetes and Alzheimer's disease.
"

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Ultrafast and downhill protein folding

medal submitted, created time 1 year 9 months (www.sciencedirect.com)

"Ultrafast folding proteins have served an important role in benchmarking molecular dynamics simulations and testing protein folding theories. These proteins are simple enough and fold fast enough that realistic simulations are possible, which facilitates the direct comparison of absolute folding rates and folding mechanisms with those observed experimentally."

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an efficient way of modeling the conformational flexibility of protein structures

seanangel submitted, created time 1 year 10 months (www.sciencedirect.com)

Researchers quality of prediction of both the magnitude and directionality of conformational flexibility. Normal modes from four simple elastic network model potentials and from the CHARMM force field are calculated for a data set of 83 diverse, ultrahigh-resolution crystal structures. While all five potentials provide good predictions of the magnitude of flexibility, all-atom potentials have a clear edge at prediction of directionality, and the CHARMM potential has the highest prediction quality

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