The DSSP program assigns protein secondary structure to one of eight states. This discrete assignment cannot describe the continuum of thermal fluctuations. Hence, a continuous assignment is proposed. Technically, the continuum results from averaging over ten discrete DSSP assignments with different hydrogen bond thresholds. The final continuous assignment for a single NMR model successfully re...

PAS (PER-ARNT-SIM) domains are a family of sensor protein domains involved in signal transduction in a wide range of organisms. Recent structural studies have revealed that these domains contain a structurally conserved alpha/beta-fold, whereas almost no conservation is observed at the amino acid sequence level. The photoactive yellow protein, a bacterial light sensor, has been proposed as the ...

a new retrofit targeting procedure, based on pinch technology has been developed. the new procedure considers existing structure of a given network and finds the most compatible configuration with the network. to achieve this aim, the procedure uses a linear programming technique that maximize the compatibility. good compatibility between old and new networks helps to make the best use of capit...

in the process of structural analysis we often come to structures that can be analyzed with simpler methods than the standard approaches. for these structures, known as regular structures, the matrices involved are in canonical forms and their eigen-solution can be performed in a simple manner. however, by adding or removing some elements or nodes, such methods cannot be utilized. here, an effi...

Abstract To realize the requirements of precision probe for translational guidance compliant mechanism, expression movement screw parallelogram guide mechanism is proposed. The flexibility matrix used to study influence geometric structure and size flexible units on performance finite element analysis simulation. results show that model in good agreement with simulation results, maximum relativ...

Protein structural fluctuation, typically measured by Debye-Waller factors, or B-factors, is a manifestation of protein flexibility, which strongly correlates to protein function. The flexibility-rigidity index (FRI) is a newly proposed method for the construction of atomic rigidity functions required in the theory of continuum elasticity with atomic rigidity, which is a new multiscale formalis...