Related papers: A Hybrid Local Search for Simplified Protein Struc…
We address protein structure prediction in the 3D Hydrophobic-Polar lattice model through two novel deep learning architectures. For proteins under 36 residues, our hybrid reservoir-based model combines fixed random projections with…
A protein is a linear chain containing a set of amino acids, which folds on itself to create a specific native structure, also called the minimum energy conformation. It is the native structure that determines the functionality of each…
Protein structure prediction (PSP) is computationally a very challenging problem. The challenge largely comes from the fact that the energy function that needs to be minimised in order to obtain the native structure of a given protein is…
The flawless functioning of a protein is essentially linked to its own three-dimensional structure. Therefore, the prediction of a protein structure from its amino acid sequence is a fundamental problem in many fields that draws researchers…
Lattice protein models, as the Hydrophobic-Polar (HP) model, are a common abstraction to enable exhaustive studies on structure, function, or evolution of proteins. A main issue is the high number of optimal structures, resulting from the…
Many proteins carry out their biological functions by forming the characteristic tertiary structures. Therefore, the search of the stable states of proteins by molecular simulations is important to understand their functions and…
In this work, we present the first implementation of the face-centered cubic (FCC) lattice model for protein structure prediction with a quantum algorithm. Our motivation to encode the FCC lattice stems from our observation that the FCC…
We demonstrate a new algorithm for finding protein conformations that minimize a non-bonded energy function. The new algorithm, called the difference map, seeks to find an atomic configuration that is simultaneously in two constraint…
A minimal off-lattice model for alpha-helical proteins is presented. It is based on hydrophobicity forces and sequence independent local interactions. The latter are chosen so as to favor the formation of alpha-helical structure. They model…
Predicting protein secondary structure using lattice model is one of the most studied computational problem in bioinformatics. Here secondary structure or three dimensional structure of protein is predicted from its amino acid sequence.…
Protein structure prediction is considered as one of the most challenging and computationally intractable combinatorial problem. Thus, the efficient modeling of convoluted search space, the clever use of energy functions, and more…
A method to search for local structural similarities in proteins at atomic resolution is presented. It is demonstrated that a huge amount of structural data can be handled within a reasonable CPU time by using a conventional relational…
A general strategy is described for finding which amino acid sequences have native states in a desired conformation (inverse design). The approach is used to design sequences of 48 hydrophobic and polar aminoacids on three-dimensional…
This paper presents a novel Differential Evolution algorithm for protein folding optimization that is applied to a three-dimensional AB off-lattice model. The proposed algorithm includes two new mechanisms. A local search is used to improve…
This paper presents a two-phase protein folding optimization on a three-dimensional AB off-lattice model. The first phase is responsible for forming conformations with a good hydrophobic core or a set of compact hydrophobic amino acid…
The hydrophobic-polar (HP) model has been widely studied in the field of protein structure prediction (PSP) both for theoretical purposes and as a benchmark for new optimization strategies. In this work we introduce a new heuristics based…
De novo protein structure prediction from amino acid sequence is one of the most challenging problems in computational biology. As one of the extensively explored mathematical models for protein folding, Hydrophobic-Polar (HP) model enables…
The precise sequence of aminoacids plays a central role in the tertiary structure of proteins and their functional properties. The Hydrophobic-Polar lattice models have provided valuable insights regarding the energy landscape. We…
Protein folding is one of the age-old biological problems that refers to the mechanism of understanding and predicting how a protein's linear sequence of amino acids folds into its specific three dimensional structure.This structure is…
Hydrophobicity is thought to be one of the primary forces driving the folding of proteins. On average, hydrophobic residues occur preferentially in the core, whereas polar residues tends to occur at the surface of a folded protein. By…