Fast search algorithms for computational protein design

Fast search algorithms for computational protein design

One of the main challenges in computational protein design (CPD) is the huge size of the protein sequence and conformational space that has to be computationally explored. Recently, we showed that state-of-the-art combinatorial optimization technologies based on Cost Function Network (CFN) processing allow speeding up provable rigid backbone protein design methods by several orders of magnitude...

Adaptive search area for fast motion estimation

In this paper a new method for determining the search area for motion estimation algorithm based on block matching is suggested. In the proposed method the search area is adaptively found for each block of a frame. This search area is similar to that of the full search (FS) algorithm but smaller for most blocks of a frame. Therefore, the proposed algorithm is analogous to FS in terms of reg...

calculation of computational complexity for radix-2p fast fourier transform algorithms for medical signals

due to its simplicity radix-2 is a popular algorithm to implement fast fourier transform. radix - 2 p algorithms have the same order of computational complexity as higher radices algorithms, but still retain the simplicity of radix-2 . by defining a new concept, twiddle factor template , in this paper we propose a method for exact calculation of multiplicative complexity for radix-2 p algorithm...

Fast Quantum Search Algorithms in Protein Sequence Comparison - Quantum Biocomputing

Quantum search algorithms are considered in the context of protein sequence comparison in biocomputing. Given a sample protein sequence of length m (i.e m residues), the problem considered is to find an optimal match in a large database containing N residues. Initially, Grover’s quantum search algorithm is applied to a simple illustrative case namely where the database forms a complete set of s...

Fast search algorithms for layout permutation problems