Search Strategies in Structural Bioinformatics

Oakley, Mark T.; Barthel, Daniel; Bykov, Yuri; Garibaldi, Jonathan M.; Burke, Edmund K.; Krasnogor, Natalio; Hirst, Jonathan D.

doi:10.2174/138920308784534032

Cited by 14 publications

(9 citation statements)

References 113 publications

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“…Such approaches modify a conformation by applying moves out of a well-defined move set . Each particular move transforms a conformation into another admissible one [2], [32]–[34], which cannot be superposed to the former (symmetries are not considered as moves). It has been widely experimented that the effectiveness of a specific Monte Carlo approach strictly depends on the used move set [35].…”

Section: Methodsmentioning

confidence: 99%

“…wiggle , see [32], sect. 4.7.2 or [2]) represents an effective way to drive a potentially radical change in the conformation, and it has been used in plenty of simulation works on bi- and three-dimensional lattices [2], [34], [40]. In practice, one residue on vertex is chosen as “pivot”, and one branch departing from it, either the forward or the backward one, is wholly rotated around to a new position.…”

Section: Methodsmentioning

confidence: 99%

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On the Characterization and Software Implementation of General Protein Lattice Models

Bechini

2013

PLoS ONE

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models of proteins have been widely used as a practical means to computationally investigate general properties of the system. In lattice models any sterically feasible conformation is represented as a self-avoiding walk on a lattice, and residue types are limited in number. So far, only two- or three-dimensional lattices have been used. The inspection of the neighborhood of alpha carbons in the core of real proteins reveals that also lattices with higher coordination numbers, possibly in higher dimensional spaces, can be adopted. In this paper, a new general parametric lattice model for simplified protein conformations is proposed and investigated. It is shown how the supporting software can be consistently designed to let algorithms that operate on protein structures be implemented in a lattice-agnostic way. The necessary theoretical foundations are developed and organically presented, pinpointing the role of the concept of main directions in lattice-agnostic model handling. Subsequently, the model features across dimensions and lattice types are explored in tests performed on benchmark protein sequences, using a Python implementation. Simulations give insights on the use of square and triangular lattices in a range of dimensions. The trend of potential minimum for sequences of different lengths, varying the lattice dimension, is uncovered. Moreover, an extensive quantitative characterization of the usage of the so-called “move types” is reported for the first time. The proposed general framework for the development of lattice models is simple yet complete, and an object-oriented architecture can be proficiently employed for the supporting software, by designing ad-hoc classes. The proposed framework represents a new general viewpoint that potentially subsumes a number of solutions previously studied. The adoption of the described model pushes to look at protein structure issues from a more general and essential perspective, making computational investigations over simplified models more straightforward as well.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

On the Characterization and Software Implementation of General Protein Lattice Models

Bechini

2013

PLoS ONE

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“…In other, intermediate models, all the atoms of the backbone are modeled, but the side chain is represented as a hard sphere centered at the center of mass of the real side chain. It has been noted however that the lower computational demands of coarse-grained models does not necessarily come at the cost of inferior expressiveness [10].…”

Section: Related Workmentioning

confidence: 99%

“…For the representational power of different common and less-common lattices, we refer the reader to [11]. On-lattice models have been chiefly used as tools for studying protein folding, because the simplified representation allows for an easier mathematical treatment [10].…”

Section: Related Workmentioning

confidence: 99%

An On/Off Lattice Approach to Protein Structure Prediction from Contact Maps

Teso

Risio

Passerini

et al. 2010

Pattern Recognition in Bioinformatics

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Abstract. An important unsolved problem in structural bioinformatics is that of protein structure prediction (PSP), the reconstruction of a biologically plausible three-dimensional structure for a given protein given only its amino acid sequence. The PSP problem is of enormous interest, because the function of proteins is a direct consequence of their three-dimensional structure. Approaches to solve the PSP use protein models that range from very realistic (all-atom) to very simple (on a lattice). Finer representations usually generate better candidate structures, but are computationally more costly than the simpler on-lattice ones. In this work we propose a combined approach that makes use of a simple and fast lattice protein structure prediction algorithm, REMC-HPPFP, to compute a number of coarse candidate structures. These are later refined by 3Distill, an off-lattice, residue-level protein structure predictor. We prove that the lattice algorithm is able to bootstrap 3Distill, which consequently converges much faster, allowing for shorter execution times without noticeably degrading the quality of the predictions. This novel method allows us to generate a large set of decoys of quality comparable to those computed by the off-lattice method alone, but using a fraction of the computations. As a result, our method could be used to build large databases of predicted decoys for analysis, or for selecting the best candidate structures through reranking techniques. Furthermore our method is generic, in that it can be applied to other algorithms than 3Distill.

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“…Several approaches have been proposed so far to deal with HP folding [17], and also exact algorithms has been found to treat sequences of reasonable length [1,9]. In a general context, the application of swarm intelligence heuristics [15] has recently gained increasing interest.…”

Section: Introductionmentioning

confidence: 99%

Cross-lattice behavior of general ACO folding for proteins in the HP model

Nardelli

Tedesco

Bechini

2013

Proceedings of the 28th Annual ACM Symposium on Applied Computing

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The computational investigation of protein folding is one of the most relevant challenges in bioinformatics. In this field, simplified lattice models for proteins like the classical HP model have been proposed, and different lattice types can be employed. A promising approach to find ground state conformations relies on Ant Colony Optimization (ACO), a popular biology-inspired heuristics: several variants have been implemented so far, on square lattices in 2D and 3D.In this paper we propose a general scheme of ACO for HP on both square and triangular lattices in 2D and 3D, including also a novel initialization procedure for the pheromone matrix according to some pre-computed suboptimal conformations. The algorithm behavior, considering the influence of the optional parts and the required parameter tuning, is investigated for the first time with experiments that systematically span different lattice types. The test outcomes are useful in understanding how to operate on the algorithm parameters.The presented results are used to sketch out general guidelines for the practical employment of ACO in conformational studies, depending on the chosen sequences and lattice types.

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Search Strategies in Structural Bioinformatics

Cited by 14 publications

References 113 publications

On the Characterization and Software Implementation of General Protein Lattice Models

On the Characterization and Software Implementation of General Protein Lattice Models

An On/Off Lattice Approach to Protein Structure Prediction from Contact Maps

Cross-lattice behavior of general ACO folding for proteins in the HP model

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