Protein preliminaries and structure prediction fundamentals for computer scientists

Abstract

Protein structure prediction is a challenging and unsolved problem in computer science. Proteins are the sequence of amino acids connected together by single peptide bond. The combinations of the twenty primary amino acids are the constituents of all proteins. In-vitro laboratory methods used in this problem are very time-consuming, cost-intensive, and failure-prone. Thus, alternative computational methods come into play. The protein structure prediction problem is to find the three-dimensional native structure of a protein, from its amino acid sequence. The native structure of a protein has the minimum free energy possible and arguably determines the function of the protein. In this study, we present the preliminaries of proteins and their structures, protein structure prediction problem, and protein models. We also give a brief overview on experimental and computational methods used in protein structure prediction. This study will provide a fundamental knowledge to the computer scientists who are intending to pursue their future research on protein structure prediction problem.

A Parallel Trajectory Swapping Wang - Landau Study Of The HP Protein Model

“…Within the same lattice dimensions and sequences used here one could study behaviour using variants of the Hamiltonian function (see equation 1). There are various HP matrices which could be investigated using this methodology for the first time (see [54] (Oct 2015) for further details). Also variants of the HOP model [47] could be generated and investigated and compare which HP energy function/matrix produces thermodynamic observables that best mimic the globular phase transitions seen in real proteins.…”