Protein Structure Prediction: Advances in Computational Methods and Their Application to Molecular Modeling

Protein structure prediction-This chapter introduces the fundamental concepts and significance of protein structure prediction, setting the stage for the discussions to follow

Alpha helix-Focuses on the alpha helix, one of the most common structural motifs in proteins, and its role in the overall stability and function of proteins

Beta sheet-Explores the beta sheet structure, its formation, and how it contributes to the protein's tertiary structure and biological function

Protein secondary structure-Delves into the various secondary structural elements in proteins, explaining their influence on protein folding and stability

Protein tertiary structure-Discusses the threedimensional arrangement of secondary structure elements and the forces that stabilize this final structure

Membrane topology-This chapter covers the prediction of membrane protein structures and their complex interactions with lipid bilayers

Structural alignment-Introduces techniques used for aligning protein structures, essential for comparing and contrasting homologous proteins

Structural bioinformatics-A look at the computational tools and methods used in protein structure prediction and analysis

Protein structure-Provides an overview of the different levels of protein structure and how they relate to function

Protein design-Discusses the principles and methods behind designing proteins with specific functions, using computational techniques

Lattice protein-Explores the concept of lattice models in protein folding, helping understand how protein structures are formed

Threading (protein sequence)-Introduces threading techniques used to predict protein structures based on sequence similarities to known structures

Protein contact map-Focuses on the use of contact maps to predict protein folding and interactions

Turn (biochemistry)-Discusses the role of turns in protein structures, their formation, and significance in maintaining protein stability

Homology modeling-This chapter explores the process of creating threedimensional models of proteins based on sequence homology

Loop modeling-Focuses on the techniques for modeling loop regions in proteins, which are crucial for function and stability

De novo protein structure prediction-Provides an indepth look at approaches used to predict protein structures without relying on homologous templates

Protein domain-Discusses the modular nature of proteins and the importance of protein domains in their structure and function

Phyre-A case study of the Phyre server, a widely used tool for protein structure prediction, explaining its applications and methods

Protein superfamily-Introduces the concept of protein superfamilies and their significance in evolutionary biology and functional prediction

ITASSER-A detailed explanation of the ITASSER tool, a powerful method for protein structure prediction that integrates multiple techniques