Algorithms for protein design

Algorithms for protein design.

Computational structure-based protein design programs are becoming an increasingly important tool in molecular biology. These programs compute protein sequences that are predicted to fold to a target structure and perform a desired function. The success of a program's predictions largely relies on two components: first, the input biophysical model, and second, the algorithm that computes the be...

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...

A Unified Approach for Design of Lp Polynomial Algorithms

By summarizing Khachiyan's algorithm and Karmarkar's algorithm forlinear program (LP) a unified methodology for the design of polynomial-time algorithms for LP is presented in this paper. A key concept is the so-called extended binary search (EBS) algorithm introduced by the author. It is used as a unified model to analyze the complexities of the existing modem LP algorithms and possibly, help ...

Design Algorithms for Doppler MTI and Filters (Using Chebyshev Approximation)

Design Algorithms for Doppler MTI and Filters (Using Chebyshev Approximation)