Computing H/D-exchange speeds of single residues from data of peptic fragments

Althaus, Ernst; Canzar, Stefan; Emmett, Mark R.; Karrenbauer, Andreas; Marshall, Alan G.; Meyer‐Baese, Anke; Zhang, Huimin

doi:10.1145/1363686.1363981

Cited by 21 publications

(64 citation statements)

References 9 publications

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“…The polyhedral description has already been introduced in [1] and has served there as a basis to attack the problem by integer programming methods and tools, which perform well in practice. Moreover, the authors established the polynomial-time solvability of the two-color case by the integrality of the polytope P and provided also a combinatorial algorithm for this case.…”

Section: Previous and Related Workmentioning

confidence: 99%

“…Another way to deal with noisy data is to model the noise in the linear programming relaxation to get a new set of requirements on which to run the algorithm from Section 2. The latter approach was explored by Althaus et al [1]; the reader is referred to their paper for details.…”

Section: Contributions Of This Papermentioning

confidence: 99%

“…The problem has been introduced recently in [1]. To be self-contained, we restrict ourselves to a very brief and informal description in this paper and refer the interested reader to the publication mentioned above.…”

Section: Introductionmentioning

confidence: 99%

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Approximating the Interval Constrained Coloring Problem

Althaus¹,

Canzar²,

Elbassioni³

et al. 2008

Algorithm Theory – SWAT 2008

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We consider the interval constrained coloring problem, which appears in the interpretation of experimental data in biochemistry. Monitoring hydrogen-deuterium exchange rates via mass spectroscopy experiments is a method used in that field to obtain information about protein tertiary structure. The output of these experiments provides data about the exchange rate of residues in overlapping fragments of the protein backbone. These fragments must be re-assembled in order to obtain a global picture of the protein structure. The interval constrained coloring problem is the mathematical abstraction of this re-assembly process.The objective of the interval constrained coloring problem is to assign a color (exchange rate) to a set of integers (protein residues) such that a set of constraints is satisfied. Each constraint is made up of a closed interval (protein fragment) and requirements on the number of elements that belong to each color class (exchange rates observed in the experiments).We show that the problem is NP-complete for arbitrary number of colors and we provide algorithms that given a feasible instance find a coloring that satisfies all the coloring requirements within ±1 of the prescribed value. In light of our first result, this is essentially the best one can hope for. Our approach is based on polyhedral theory techniques and randomized rounding. Furthermore, we develop a quasi-polynomial-time approximation scheme for a variant of our problem where we are asked to find a coloring satisfying as many as fragments as possible.

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Section: Previous and Related Workmentioning

confidence: 99%

Section: Contributions Of This Papermentioning

confidence: 99%

See 1 more Smart Citation

Approximating the Interval Constrained Coloring Problem

Althaus¹,

Canzar²,

Elbassioni³

et al. 2008

Algorithm Theory – SWAT 2008

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show abstract

“…Althaus et al [4] formulated the problem of improving the resolution of exchange data as a linear minimization problem subject to integer linear constraints (ILP) and described an algorithm that often assigns deuterium exchange rates with single amino acid resolution. Based on this formulation, a branch and bound-based approach was given to enumerate all possible exchange rates for single residues.…”

Section: Related Work and Comparison To Our Workmentioning

confidence: 99%

“…While the approach used in [4] is somewhat related to ours, there are some fundamental differences. First, our algorithm does not only produce exact solutions, but may also produce approximate solutions, in which case each component of the approximate solution is guaranteed to be within an absolute error of 1 of the optimal error.…”

Section: Related Work and Comparison To Our Workmentioning

confidence: 99%

A polynomial-delay algorithm for enumerating approximate solutions to the interval constrained coloring problem

Canzar

Elbassioni²,

Mestre

2013

ACM J. Exp. Algorithmics

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We study the interval constrained coloring problem, a combinatorial problem arising in the interpretation of data on protein structure emanating from experiments based on hydrogen/deuterium exchange and mass spectrometry. The problem captures the challenging task of increasing the spatial resolution of experimental data in order to get a better picture of the protein structure. Since solutions proposed by any algorithmic framework have to ultimately be verified by biochemists, it is important to provide not just a single solution, but a valuable set of candidate solutions. Our contribution is a polynomial delay, polynomial space algorithm for enumerating all exact solutions plus further approximate solutions, whose components are guaranteed to be within an absolute error of one of the optimum. Our experiments indicate that these approximate solutions are reasonably close to the optimal ones, in terms of the accumulative error. On the other hand, the experiments also confirm the effectiveness of the method in producing solutions much faster than what it takes an integer programming solver to produce an exact solution.

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Data analysis techniques in phosphoproteomics

et al. 2014

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The interpretation of phosphoproteomics data sets is crucial for generating hypotheses that guide therapeutic solutions, yet not many techniques have been applied to this type of analysis. This paper intends to give an overview about the two main standard techniques that can be applied to the analysis of these large scale data sets. These are data-driven or exploratory techniques based on a statistical model and topology-driven methods that analyze the signaling network from a dynamical standpoint. While employing different paradigms, these algorithms will detect unique "fingerprints" by revealing the intricate interactions at the proteome level and will support the experimental environment for novel therapeutics for many diseases.

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Computing H/D-exchange speeds of single residues from data of peptic fragments

Cited by 21 publications

References 9 publications

Approximating the Interval Constrained Coloring Problem

Approximating the Interval Constrained Coloring Problem

A polynomial-delay algorithm for enumerating approximate solutions to the interval constrained coloring problem

Data analysis techniques in phosphoproteomics

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