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

@inproceedings{Nardelli2013CrosslatticeBO,
  title={Cross-lattice behavior of general ACO folding for proteins in the HP model},
  author={Mimma Nardelli and Luciano Tedesco and Alessio Bechini},
  booktitle={SAC '13},
  year={2013}
}
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… 
View on ACM
doi.org
10 Citations
Background Citations
2
Methods Citations
2

Figures and Tables from this paper

10 Citations

Citation Type

Citation Type

On the Characterization and Software Implementation of General Protein Lattice Models
TLDR
A new general parametric lattice model for simplified protein conformations is proposed and investigated, and 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.
A Firefly-Inspired Method for Protein Structure Prediction in Lattice Models
TLDR
A Firefly-inspired algorithmic approach for protein structure prediction over two different lattice models in three-dimensional space, with the aim of justifying future research on larger instances within lattice model settings, eventually leading to the ultimate goal of implementations for off-lattice models.
Hybrid method to solve HP model on 3D lattice and to probe protein stability upon amino acid mutations
TLDR
A novel hybrid method to combine several heuristic strategies to study HP model on 3D lattice can predict protein structure more accurately and efficiently and serves as a useful tools to probe the protein stability on 3d lattice and provides some biological insights.
A benchmark of optimally folded protein structures using integer programming and the 3D-HP-SC model
Exact methods for lattice protein models
TLDR
Fundamental concepts like hydrophobic core construction and their use in optimal structure prediction, as well as possible applications like combinations of different energy models are discussed.
Constraint-handling through multi-objective optimization: The hydrophobic-polar model for protein structure prediction
PinaColada: peptide-inhibitor ant colony ad-hoc design algorithm
TLDR
PinaColada is a novel computational method for the design of peptide inhibitors for protein-protein interactions that employs a version of the ant colony optimization heuristic, which is used to explore the exponential space of length n peptide sequences, in combination with the fast robotics motivated PepCrawler algorithm, which explores the conformational space for each candidate sequence.
Multi-objectivization, fitness landscape transformation and search performance: A case of study on the hp model for protein structure prediction
Protein-Peptide Interaction Design: PepCrawler and PinaColada.
TLDR
This chapter presents two methods related to rational design of inhibitory peptides: PepCrawler: A tool to derive binding peptides from protein-protein complexes and the prediction of protein-peptide complexes and PinaColada: A peptide design program for the discovery of novel peptide candidates that inhibit protein- protein interactions.
ACOTSP-MF: A memory-friendly and highly scalable ACOTSP approach

References

SHOWING 1-10 OF 23 REFERENCES
On the Characterization and Software Implementation of General Protein Lattice Models
TLDR
A new general parametric lattice model for simplified protein conformations is proposed and investigated, and 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.
An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem
TLDR
The application of ACO to this bioinformatics problem compares favourably with specialised, state-of-the-art methods for the 2D and 3D HP protein folding problem; the empirical results indicate that the rather simple ACO algorithm scales worse with sequence length but usually finds a more diverse ensemble of native states.
On Lattice Protein Structure Prediction Revisited
TLDR
A Large Neighborhood Search to find the native state for the Hydrophobic-Polar model on the Face-Centered Cubic (FCC) lattice or, in other words, a self-avoiding walk on the FCC lattice having a maximum number of H-H contacts.
An Improved Ant Colony Optimisation Algorithm for the 2D HP Protein Folding Problem
TLDR
An improved version of the recently proposed Ant Colony Optimisation (ACO) algorithm for this NP-hardcom binatorial problem is presented and its ability to solve standard benchmark instances substantially better than the original algorithm is demonstrated.
Parallel ant colony optimization for 3D protein structure prediction using the HP lattice model
TLDR
A novel method of solving the HP protein folding problem in both two and three dimensions is introduced using ant colony optimizations and a distributed programming paradigm.
A Constraint-Based Approach to Fast and Exact Structure Prediction in Three-Dimensional Protein Models
TLDR
This approach is the first one that can be applied to two three-dimensional lattices, namely the cubic lattice and the face-centered-cubic (FCC) lattice, and it is the only exact method for the FCC lattice.
An Effective Exact Algorithm and a New Upper Bound for the Number of Contacts in the Hydrophobic-Polar Two-Dimensional Lattice Model
TLDR
An innovative algorithm is presented that outperforms the state of the art in exact approaches for the prediction of optimal structures in lattice protein model, for 2D square lattices, and provides the degeneracy of such benchmark sequences, which was unknown in literature.
Search strategies in structural bioinformatics.
TLDR
This review describes recent work addressing a selection of bioinformatics challenges, and highlights the use of memetic algorithms, which combine genetic algorithms with local optimisation, to the study of simple protein models on the two-dimensional square lattice and the face-centred cubic lattice.
Comparative modeling and protein‐like features of hydrophobic–polar models on a two‐dimensional lattice
TLDR
This study considers two different hydrophobic–polar (HP) models on the 2D square lattice: the purely HP model and a model where a compactness‐favoring term is added, which suggest that lattice models incorporate the fundamental physical principles of proteins.
Protein Folding in the HP-Model Solved With a Hybrid Population Based ACO Algorithm
TLDR
A hybrid population based Ant Colony Optimization (ACO) algorithm PFold-P-ACO for protein folding in the HP model is proposed and it is shown experimentally that the algorithms achieves on nearly all test sequences at least comparable results to other state of the art algorithms.
...
1
2
3
...