A Review of Protein Structure Prediction Using Lattice Model

Abstract

The prediction of the tertiary structure of a protein from its primary sequence is a long-standing problem for life science researchers. Solutions to this problem have a direct impact on other research areas such as design and discovery of new drugs, understanding the sequenced genomic data, solving the puzzle of protein structure, and understanding the folding mechanism. Solving protein structure prediction (PSP) is considered a cornerstone for life science research to reveal the mechanism of cellular processes; it has been an open problem for past six decades. Globally, various research institutes are working toward a solution to PSP with different methods. In this paper, we present a review of de novo PSP using hydrophobic-polar lattice model. In the hydrophobic-polar model, the PSP problem is defined as a combinatorial optimization problem with an objective of finding the protein structure having the lowest free energy. This study is bounded to two key factors. The first is application of the evolutionary search algorithms for PSP, and the second is the evolution of the modeling method and its corresponding potential energy function. The goal of this paper is to give sufficient biological background to understand the fundamentals of proteins, their structure, and available computational methods.

A Bioinformatic Approach for Molecular Characterization and Functional Annotation of an Uncharacterized Protein from Vibrio cholerae

“…In the case of the anticipated tertiary structure by the Swiss Model, the assessment experiment executed by the Ramachandran Map (PROCHECK) indicated that 93% of the total residues (227) were found in the core, 7.0% of residues were found in the additional allowed regions, and there was no residue found in the abundantly authorized parts and the disallowed areas [22,23]. The number of non-glycine and non-proline residues was 244, which was 100%, and the end residues were four; the glycine and proline residues were 20 and 8, respectively, among the 276 total residues (Figure 1).…”

Lattice-based Monte Carlo simulation of the effects of nutrient concentration and magnetic field exposure on yeast colony growth and morphology

“…One well-known application is the Ising model of ferromagnetism in statistical mechanics [15]. In biophysics, protein folding is commonly described by a class of lattice models of compact polymers in which the constituent amino acids are constrained to occupy a regular array of positions in space [16,17]. Lattice-based models have also been used to model cellular proliferation and migration, as well as pattern formation [18,19].…”

Preface: Biomedical Engineering Research at Manipal Academy of Higher Education and Kasturba Medical College, Mangaluru

“…The hydrophobic-polar (HP) model is one of the most widely accepted models to study protein folding and the PSP problem at a coarse level. 4 Although, the HP model has reduced the complexity of the PSP problem, the possible search space is vast. Dubey et al provide solutions in the second paper entitled, "A Comparative Study on Single and Multiple Point Crossovers in Genetic Algorithms for Coarse Protein Modeling."…”