Related papers: A Novel Method for Sampling Alpha-Helical Protein …
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…
Recently, we presented a framework for understanding protein structure based on the idea that simple constructs of holding hands or touching of objects can be used to rationalize the common characteristics of globular proteins. We developed…
The Automated Protein Structure Analysis (APSA) method, which describes the protein backbone as a smooth line in 3-dimensional space and characterizes it by curvature kappa and torsion tau as a function of arc length s, was applied on 77…
Protein tertiary structure defines its functions, classification and binding sites. Similar structural characteristics between two proteins often lead to the similar characteristics thereof. Determining structural similarity accurately in…
Protein one-dimensional (1D) structures such as secondary structure and contact number provide intuitive pictures to understand how the native three-dimensional (3D) structure of a protein is encoded in the amino acid sequence. However, it…
Despite the variety of protein sizes, shapes, and backbone configurations found in nature, the design of novel protein folds remains an open problem. Within simple lattice models it has been shown that all structures are not equally…
The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the…
Motivation Protein fold recognition is an important problem in structural bioinformatics. Almost all traditional fold recognition methods use sequence (homology) comparison to indirectly predict the fold of a tar get protein based on the…
Understanding and extracting the patterns of microscopy images has been a major challenge in the biomedical field. Although trained scientists can locate the proteins of interest within a human cell, this procedure is not efficient and…
Atomic packing is an important metric for characterizing protein structures, as it significantly influences various features including the stability, the rate of evolution and the functional roles of proteins. Packing in protein structures…
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…
The remarkable structural diversity of modern proteins reflects millions of years of evolution, during which sequence space has expanded while many structural features remain conserved. This conservation is evident not only among homologous…
Proteins are the basic building blocks of life. They usually perform functions by folding to a particular structure. Understanding the folding process could help the researchers to understand the functions of proteins and could also help to…
We have exactly enumerated all sequences and conformations of HP proteins with chains of up to 19 monomers on the simple cubic lattice. For two variants of the hydrophobic-polar (HP) model, where only two types of monomers are…
Is protein secondary structure primarily determined by local interactions between residues closely spaced along the amino acid backbone, or by non-local tertiary interactions? To answer this question we have measured the entropy densities…
Protein structure prediction based on Hydrophobic-Polar energy model essentially becomes searching for a conformation having a compact hydrophobic core at the center. The hydrophobic core minimizes the interaction energy between the amino…
Background:Prediction of protein three-dimensional structures from amino acid sequences is a long-standing goal in computational/molecular biology. The successful discrimination of protein folds would help to improve the accuracy of protein…
We describe the results obtained from an improved model for protein folding. We find that a good agreement with the native structure of a 46 residue long, five-letter protein segment is obtained by carefully tuning the parameters of the…
The ability to engineer optimized protein variants has transformative potential for biotechnology and medicine. Prior sequence-based optimization methods struggle with the high-dimensional complexities due to the epistasis effect and the…
The Gene or DNA sequence in every cell does not control genetic properties on its own; Rather, this is done through translation of DNA into protein and subsequent formation of a certain 3D structure. The biological function of a protein is…