Protein Threading
نویسندگان
چکیده
The most important in silico methods, to exploit the amount of new genomic data, are based on the concept of homology. The principle of homology-based analysis is to identify a homology relationship between a new protein and a protein whose function is known. For remote homologs, sequence alignment methods fail. In such a case one aligns the sequence of a new protein with the 3D structures of known proteins. Such methods are called fold recognition methods or threading methods.
منابع مشابه
Clique-based algorithms for protein threading with profiles and constraints
Protein threading with profiles in which constraints on distances between residues are given is known to be NP-hard. Moreover, a simple algorithm known as CLIQUETHREAD based on efficient reduction to maximum edge-weight clique finding problem has been known to be a practical algorithm for solving the protein threading problem with profiles and constraints. This algorithm is not efficient enough...
متن کاملDynamic Programming and Clique Based Approaches for Protein Threading with Profiles and Constraints
The protein threading problem with profiles is known to be efficiently solvable using dynamic programming. In this paper, we consider a variant of the protein threading problem with profiles in which constraints on distances between residues are given. We prove that protein threading with profiles and constraints is NP-hard. Moreover, we show a strong hardness result on the approximation of an ...
متن کاملProtein Threading by Linear Programming
Protein three-dimensional structure prediction through threading approach has been extensively studied and various models and algorithms have been proposed. In order to further explore ways to improve accuracy and efficiency of the threading process, this paper investigates the effectiveness of a new method: protein threading via linear programming. Based on the contact map model of protein 3D ...
متن کاملAlgorithmic Aspects of Protein Threading
This chapter provides an overview of computational problems and techniques for protein threading. Protein threading is one of the most powerful approaches to protein structure prediction, where protein structure prediction is to infer three-dimensional (3-D) protein structure for a given protein sequence. Protein threading can be modeled as an optimization problem. Optimal solutions can be obta...
متن کاملBoosting Protein Threading Accuracy
Protein threading is one of the most successful protein structure prediction methods. Most protein threading methods use a scoring function linearly combining sequence and structure features to measure the quality of a sequence-template alignment so that a dynamic programming algorithm can be used to optimize the scoring function. However, a linear scoring function cannot fully exploit interdep...
متن کاملAlgorithms for Computing an Optimal Protein Threading with Profiles and Distance Restraints
Protein threading is one of the powerful methods for protein structure prediction. Some advances are recently made by the significant utilization of distance restraints. Xu et al. proposed a protein threading method in which distance constraints obtained from NMR experiments were taken into account [5]. Young et al. recently developed a novel experimental method to increase the predictive accur...
متن کامل