Protein folding in HP model on hexagonal lattices with diagonals

Shaw, Dipan; Islam, Akm Saiful; Rahman, M. Sohel; Hasan, Masud

doi:10.1186/1471-2105-15-s2-s7

Cited by 9 publications

(6 citation statements)

References 14 publications

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“…In summary, taken together our 1764 inspections intend to contribute with better criteria in the conformational ensemble selection, capture protein fundamental aspects and furnish structural-interactional insights for native conformations of homologous proteins, as well as support the inference that our rule-based approach can potentially to be applied to study other proteins and to better understand conformational variability in biomolecular processes such as protein evolution, design, dynamics and folding [29,[45][46][47][48][49]. Such inspections obtained via two coarse-grained models work complementally with other results from simplified approaches, including misfolding and unfolding events [50], comparative modeling to explore protein-like features [51], lattice models for protein folding [52], energy landscape mapping methods for structure predictions [53], and evaluation of knots in proteins [54]. Furthermore our approach intend to join with other tools and resources [55][56][57][58] to help researches in the protein sequence-structure correlations and to pave the way for improving the general understanding of conformational ensembles in further proteins.…”

Section: Resultssupporting

confidence: 66%

Structural, Conformational and Interactional Investigation of Proteins with Related Sequences and Multiple Structures

Eller¹

2018

IJBBMB

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Homologous proteins are special macromolecules with related primary sequences and multiple native structures and together with sequence-unrelated nonhomologous ones both constitute the protein amazing universe. Here is made a thorough sample selection, and employed quantitative predictions to analyze structures, conformations, steric and hydrophobic interactions and underlying molecular mechanisms in proteins via two coarse-grained (hydrophobic-polar, large-small) models. First, five empirical relations from nonhomologous samples are determined correlating large and hydrophobic residue sequences from primary to helix and β-sheet structures of functional conformations. When applied to homologous proteins, such empirical relations allow precisely surveying the interaction performance, identifying four types of molecular mechanisms, and computing the stability level in conformation ensembles. 1764 structural inspections capture essential features and furnish structural-interactional insights for homologous proteins, as well as suggest a fruitful way for better understanding conformational variability in biomolecular processes such as protein evolution, dynamics, folding and design.

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Section: Resultssupporting

confidence: 66%

Structural, Conformational and Interactional Investigation of Proteins with Related Sequences and Multiple Structures

Eller¹

2018

IJBBMB

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“…We postulate that in the future, a hybrid approach based on both geometric and physical models will be possible. Shaw et al, 2014 considered protein folding on a hexagonal lattice using the HP model. The authors divided the lattice folding models into two classes: simplified lattice models and realistic lattice models.…”

Section: Geometrical Models Of Protein Foldingmentioning

confidence: 99%

On a generalized Levinthal's paradox: The role of long- and short range interactions in complex bio-molecular reactions, including protein and DNA folding

Melkikh

Meijer

2018

Progress in Biophysics and Molecular Biology

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The current protein folding literature is reviewed. Two main approaches to the problem of folding were selected for this review: geometrical and biophysical. The geometrical approach allows the formulation of topological restrictions on folding, that are usually not taken into account in the construction of physical models. In particular, the topological constraints do not allow the known funnel-like energy landscape modeling, although most common methods of resolving the paradox are based on this method. The very paradox is based on the fact that complex molecules must reach their native conformations (complexes that result from reactions) in an exponentially long time, which clearly contradicts the observed experimental data. In this respect we considered the complexity of the reactions between ligands and proteins. On this general basis, the folding-reaction paradox was reformulated and generalized. We conclude that prospects for solving the paradox should be associated with incorporating a topology aspect in biophysical models of protein folding, through the construction of hybrid models. However, such models should explicitly include long-range force fields and local cell biological conditions, such as structured water complexes and photon/phonon/soliton waves, ordered in discrete frequency bands. In this framework, collective and coherent oscillations in, and between, macromolecules are instrumental in inducing intra- and intercellular resonance, serving as an integral guiding network of life communication: the electrome aspect of the cell. Yet, to identify the actual mechanisms underlying the bonds between molecules (atoms), it will be necessary to perform dedicated experiments to more definitely solve the particular time paradox.

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“…A description of exact methods may be found in the review [Mann and Backofen, 2014]. Many variants of the HP model exist that enable for instance diagonals (triangular lattice), work in an hexagonal lattice [Shaw et al, 2014] or in a face-centered cubic lattice (fcc, one of the best models in this category [Pokarowski et al, 2003;Shatabda et al, 2014]). Other moderate resolution lattices exist, using a larger basis of vectors for the definition of the neighborhood.…”

Section: Folding In Spacementioning

confidence: 99%

Artificial Intelligence and Bioinformatics

Nicolas

2020

A Guided Tour of Artificial Intelligence Research

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HAL is a multidisciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

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Protein folding in HP model on hexagonal lattices with diagonals

Cited by 9 publications

References 14 publications

Structural, Conformational and Interactional Investigation of Proteins with Related Sequences and Multiple Structures

Structural, Conformational and Interactional Investigation of Proteins with Related Sequences and Multiple Structures

On a generalized Levinthal's paradox: The role of long- and short range interactions in complex bio-molecular reactions, including protein and DNA folding

Artificial Intelligence and Bioinformatics

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