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430
Protein Threading
- SUBMISSION TO: THE PROTEOMICS HANDBOOK
"... Given a protein's sequence, one may try to predict its structure by reference to basic physics or even by searching against some more pragmatic quasi-energy or score function. Threading attempts to solve what should be a simpler problem – looking through the set of currently known structures an ..."
Abstract
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Cited by 2 (0 self)
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Given a protein's sequence, one may try to predict its structure by reference to basic physics or even by searching against some more pragmatic quasi-energy or score function. Threading attempts to solve what should be a simpler problem – looking through the set of currently known structures
Protein Threading by Linear Programming
- Biocomputing: Proceedings of the 2003 Paci Symposium
, 2003
"... this paper investigates the effectiveness of a new method: protein threading via linear programming. Based on the contact map model of protein 3D structure we formulate the protein threading problem as a large scale integer programming problem then relax to a linear programming problem and final ..."
Abstract
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Cited by 19 (9 self)
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this paper investigates the effectiveness of a new method: protein threading via linear programming. Based on the contact map model of protein 3D structure we formulate the protein threading problem as a large scale integer programming problem then relax to a linear programming problem
On the approximation of protein threading
- Theoretical Computer Science
, 1999
"... In this paper, we study the protein threading problem, which was proposed for predicting a folded 3D protein structure from an amino acid sequence. Since this problem was already proved to be NP-hard, we study polynomial time approximation algorithms. We show several hardness results for the approxi ..."
Abstract
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Cited by 30 (2 self)
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In this paper, we study the protein threading problem, which was proposed for predicting a folded 3D protein structure from an amino acid sequence. Since this problem was already proved to be NP-hard, we study polynomial time approximation algorithms. We show several hardness results
Low-homology protein threading
- Bioinformatics 2010
"... Motivation: The challenge of template-based modeling lies in the recognition of correct templates and generation of accurate sequence-template alignments. Homologous information has proved to be very powerful in detecting remote homologs, as demonstrated by the state-of-the-art profile-based method ..."
Abstract
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Cited by 9 (1 self)
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for low-homology protein threading. This method will model correlation among various protein features and determine their relative importance according to the amount of homologous information available. When proteins under consideration are low-homology, our method will rely more on structure information
Genetic algorithms for protein threading
- Proc. Int. Conf. Intell. Syst. Mol. Biol
, 1998
"... Despite many years of efforts, a direct prediction of protein structure from sequence is still not possible. As a result, in the last few years researchers have started to address the “inverse folding problem": Identifying and aligning a sequence to the fold with which it is most compatible, a ..."
Abstract
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Cited by 4 (1 self)
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process known as “threading”. In two meetings in which protein folding predictions were objectively evaluated, it became clear that threading as a concept promises a real breakthrough, but that much improvement is still needed in the technique itself. Threading is a NP-hard problem, and thus no general
Solving the Protein Threading Problem in Parallel
- In IPDPS ’03: Proceedings of the 17th International Symposium on Parallel and Distributed Processing
, 2003
"... We propose a network flow formulation for protein threading and show its equivalence with the shortest path problem on a graph with a very particular structure. The underying Mixed Integer Programming (MIP) model proves to be very appropriate for the protein threading problem--huge real-life instanc ..."
Abstract
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Cited by 8 (4 self)
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We propose a network flow formulation for protein threading and show its equivalence with the shortest path problem on a graph with a very particular structure. The underying Mixed Integer Programming (MIP) model proves to be very appropriate for the protein threading problem--huge real
Optimal protein threading by cost-splitting
- In Proceedings of the Annual Workshop on Algorithms in Bioinformatics (WABI
, 2005
"... Abstract. In this paper, we use integer programming approach for solv-ing a hard combinatorial optimization problem, namely protein thread-ing. For this sequence-to-structure alignment problem we apply cost-splitting technique to derive a new Lagrangian dual formulation. The optimal solution of the ..."
Abstract
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Cited by 6 (4 self)
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Abstract. In this paper, we use integer programming approach for solv-ing a hard combinatorial optimization problem, namely protein thread-ing. For this sequence-to-structure alignment problem we apply cost-splitting technique to derive a new Lagrangian dual formulation. The optimal solution
The Protein Threading Problem With Sequence Amino Acid Interaction Preferences Is NP-Complete
- Protein Eng
, 1995
"... In recent protein structure prediction research there has been a great deal of interest in using amino acid interaction preferences (e.g., contact potentials, or potentials of mean force) to align ("thread") a protein sequence to a known structural motif. An important open question is whet ..."
Abstract
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Cited by 122 (4 self)
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In recent protein structure prediction research there has been a great deal of interest in using amino acid interaction preferences (e.g., contact potentials, or potentials of mean force) to align ("thread") a protein sequence to a known structural motif. An important open question
Results 1 - 10
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430
