CPSP-tools – Exact and complete algorithms for high-throughput 3D lattice protein studies

Mann, Martin; Will, Sebastian; Backofen, Rolf

doi:10.1186/1471-2105-9-230

Cited by 49 publications

(56 citation statements)

References 30 publications

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“…Among them are the extension to the HPNX model [46,75] or to side-chain structure models [44], both later discussed in detail. In contrast to most tools and approaches in the field, a CPSP implementation is available for local installation [45,76] and ad hoc web usage [44,77]. Thus, it has spawned the compilation of extensive benchmark data sets of protein-like sequences with various folding features [78].…”

Section: Constraint-based Protein Structure Predictionmentioning

confidence: 99%

“…Its basic version is tailored for 3D backbone-only HP models [43,45,73,74] but was extended to other models. Among them are the extension to the HPNX model [46,75] or to side-chain structure models [44], both later discussed in detail.…”

Section: Constraint-based Protein Structure Predictionmentioning

confidence: 99%

“…While the CHCC approach was the first exact PSP method, it was proven to be incomplete when enumerating all optimal structures [43]. In contrast, the constraint-based protein structure prediction (CPSP) approach [43][44][45] was shown to be exact and complete when calculating optimal structures. CPSP uses a similar strategy as CHCC and is thus far the only exact and complete method for protein structure prediction in lattice protein models.…”

Section: Introductionmentioning

confidence: 95%

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Exact methods for lattice protein models

Mann

Backofen²

2014

Bio-Algorithms and Med-Systems

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Lattice protein models are well-studied abstractions of globular proteins. By discretizing the structure space and simplifying the energy model over regular proteins, they enable detailed studies of protein structure formation and evolution. However, even in the simplest lattice protein models, the prediction of optimal structures is computationally difficult. Therefore, often, heuristic approaches are applied to find such conformations.Commonly, heuristic methods find only locally optimal solutions. Nevertheless, there exist methods that guarantee to predict globally optimal structures. Currently, only one such exact approach is publicly available, namely the constraint-based protein structure prediction method and variants. Here, we review exact approaches and derived methods. We discuss fundamental concepts like hydrophobic core construction and their use in optimal structure prediction, as well as possible applications like combinations of different energy models.

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Section: Constraint-based Protein Structure Predictionmentioning

confidence: 99%

Section: Constraint-based Protein Structure Predictionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 95%

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Exact methods for lattice protein models

Mann

Backofen²

2014

Bio-Algorithms and Med-Systems

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“…The HP model has been extended in several directions. Beside square and simple cubic lattices, other common lattices structures were considered, for instance the triangular and face centred cubic lattices [17,18]. Furthermore, side chains were taken into account [19].…”

Section: The Hydrophobic-polar Model Of Protein Foldingmentioning

confidence: 99%

Structure optimisation by thermal cycling for the hydrophobic-polar lattice model of protein folding

Günther

Möbius

Schreiber

2017

Eur. Phys. J. Spec. Top.

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Abstract. The function of a protein depends strongly on its spatial structure. Therefore the transition from an unfolded stage to the functional fold is one of the most important problems in computational molecular biology. Since the corresponding free energy landscapes exhibit huge numbers of local minima, the search for the lowest-energy configurations is very demanding. Because of that, efficient heuristic algorithms are of high value. In the present work, we investigate whether and how the thermal cycling (TC) approach can be applied to the hydrophobic-polar (HP) lattice model of protein folding. Evaluating the efficiency of TC for a set of two-and three-dimensional examples, we compare the performance of this strategy with that of multi-start local search (MSLS) procedures and that of simulated annealing (SA). For this aim, we incorporated several simple but rather efficient modifications into the standard procedures: in particular, a strong improvement was achieved by also allowing energy conserving state modifications. Furthermore, the consideration of ensembles instead of single samples was found to greatly improve the efficiency of TC. In the framework of different benchmarks, for all considered HP sequences, we found TC to be far superior to SA, and to be faster than Wang-Landau sampling.

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“…Some of them are pretty efficient, such as Gecode, which has been used in many research projects in last the years [8] [9]. In this paper, we model a mission planning problem as a TCSP for a team of UAVs, using Gecode as the CSP modeller to program the constraints of the problem, and solve them using Backtracking (BT) search.…”

Section: Introductionmentioning

confidence: 99%

A simple CSP-based model for Unmanned Air Vehicle Mission Planning

Ramírez-Atencia

Bello-Orgaz

R-Moreno

et al. 2014

2014 IEEE International Symposium on Innovations in Intelligent Systems and Applications (INISTA) Proceedings

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Esta es la versión de autor de la comunicación de congreso publicada en: This is an author produced version of a paper published in: Abstract-The problem of Mission Planning for a large number of Unmanned Air Vehicles (UAV) can be formulated as a Temporal Constraint Satisfaction Problem (TCSP). It consists on a set of locations that should visit in different time windows, and the actions that the vehicle can perform based on its features such as the payload, speed or fuel capacity. In this paper, a temporal constraint model is implemented and tested by performing Backtracking search in several missions where its complexity has been incrementally modified. The experimental phase consists on two different phases. On the one hand, several mission simulations containing (n) UAVs using different sensors and characteristics located in different waypoints, and (m) requested tasks varying mission priorities have been carried out. On the other hand, the second experimental phase uses a backtracking algorithm to look through the whole solutions space to measure the scalability of the problem. This scalability has been measured as a relation between the number of tasks to be performed in the mission and the number of UAVs needed to perform it.

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CPSP-tools – Exact and complete algorithms for high-throughput 3D lattice protein studies

Cited by 49 publications

References 30 publications

Exact methods for lattice protein models

Exact methods for lattice protein models

Structure optimisation by thermal cycling for the hydrophobic-polar lattice model of protein folding

A simple CSP-based model for Unmanned Air Vehicle Mission Planning

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