Potential function of simplified protein models for discriminating native proteins from decoys: Combining contact interaction and local sequence-dependent geometry

An effective potential function is critical for protein structure prediction and folding simulation. For simplified models of proteins where coordinates of only $C_\alpha$ atoms need to be specified, an accurate potential function is important. Such a simplified model is essential for efficient search of conformational space. In this work, we present a formulation of potential function for simplified representations of protein structures. It is based on the combination of descriptors derived from residue-residue contact and sequence-dependent local geometry. The optimal weight coefficients for contact and local geometry is obtained through optimization by maximizing margins among native and decoy structures. The latter are generated by chain growth and by gapless threading. The performance of the potential function in blind test of discriminating native protein structures from decoys is evaluated using several benchmark decoy sets. This potential function have comparable or better performance than several residue-based potential functions that require in addition coordinates of side chain centers or coordinates of all side chain atoms.Comment: 4 pages, 2 figures, Accepted by 26th IEEE-EMBS Conference, San Francisc

Error probability and capacity analysis of generalised pre-coding aided spatial modulation

The recently proposed multiple input multiple output (MIMO) transmission scheme termed as generalized pre-coding aided spatial modulation (GPSM) is analyzed, where the key idea is that a particular subset of receive antennas is activated and the specific activation pattern itself conveys useful implicit information. We provide the upper bound of both the symbol error ratio (SER) and bit error ratio (BER) expression of the GPSM scheme of a low-complexity decoupled detector. Furthermore, the corresponding discrete-input continuous-output memoryless channel (DCMC) capacity as well as the achievable rate is quantified. Our analytical SER and BER upper bound expressions are confirmed to be tight by our numerical results. We also show that our GPSM scheme constitutes a flexible MIMO arrangement and there is always a beneficial configuration for our GPSM scheme that offers the same bandwidth efficiency as that of its conventional MIMO counterpart at a lower signal to noise ratio (SNR) per bit