arXiv subjects

Isabel Houtkamp

Publications and source records attributed to Isabel Houtkamp.

4 recordsLinked to original sources

arXiv2023

Structural Property Prediction

While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims to give an introduction into Structural Bioinformatics, which is where the previous topics meet to explore three dimensional protein structures through computational analysis. We provide an overview of existing computational techniques, to validate, simulate, predict and analyse protein structures. More importantly, it will aim to provide practical knowledge about how and when to use such techniques. We will consider proteins from three major vantage points: Protein structure quantification, Protein structure prediction, and Protein simulation & dynamics. Some structural properties of proteins that are closely linked to their function may be easier (or much faster) to predict from sequence than the complete tertiary structure; for example, secondary structure, surface accessibility, flexibility, disorder, interface regions or hydrophobic patches. Serving as building blocks for the native protein fold, these structural properties also contain important structural and functional information not apparent from the amino acid sequence. Here, we will first give an introduction into the application of machine learning for structural property prediction, and explain the concepts of cross-validation and benchmarking. Next, we will review various methods that incorporate knowledge of these concepts to predict those structural properties, such as secondary structure, surface accessibility, disorder and flexibility, and aggregation.

q-bio.BM↗

arXiv2023

Structure Alignment

While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims to give an introduction into Structural Bioinformatics, which is where the previous topics meet to explore three dimensional protein structures through computational analysis. We provide an overview of existing computational techniques, to validate, simulate, predict and analyse protein structures. More importantly, it will aim to provide practical knowledge about how and when to use such techniques. We will consider proteins from three major vantage points: Protein structure quantification, Protein structure prediction, and Protein simulation & dynamics. The Protein DataBank (PDB) contains a wealth of structural information. In order to investigate the similarity between different proteins in this database, one can compare the primary sequence through pairwise alignment and calculate the sequence identity (or similarity) over the two sequences. This strategy will work particularly well if the proteins you want to compare are close homologs. However, in this chapter we will explain that a structural comparison through structural alignment will give you much more valuable information, that allows you to investigate similarities between proteins that cannot be discovered by comparing the sequences alone.

q-bio.BM↗

arXiv2023

Introduction to Protein Folding

While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims to give an introduction into Structural Bioinformatics, which is where the previous topics meet to explore three dimensional protein structures through computational analysis. We provide an overview of existing computational techniques, to validate, simulate, predict and analyse protein structures. More importantly, it will aim to provide practical knowledge about how and when to use such techniques. We will consider proteins from three major vantage points: Protein structure quantification, Protein structure prediction, and Protein simulation & dynamics. In this chapter we explore basic physical and chemical concepts required to understand protein folding. We introduce major (de)stabilising factors of folded protein structures such as the hydrophobic effect and backbone entropy. In addition, we consider different states along the folding pathway, as well as natively disordered proteins and aggregated protein states. In this chapter, an intuitive understanding is provided about the protein folding process, to prepare for the next chapter on the thermodynamics of protein folding. In particular, it is emphasized that protein folding is a stochastic process and that proteins unfold and refold in a dynamic equilibrium. The effect of temperature on the stability of the folded and unfolded states is also explained.

q-bio.BM↗

arXiv2023

Thermodynamics of Protein Folding

While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims to give an introduction into Structural Bioinformatics, which is where the previous topics meet to explore three dimensional protein structures through computational analysis. We provide an overview of existing computational techniques, to validate, simulate, predict and analyse protein structures. More importantly, it will aim to provide practical knowledge about how and when to use such techniques. We will consider proteins from three major vantage points: Protein structure quantification, Protein structure prediction, and Protein simulation & dynamics. In the previous chapter, "Introduction to Protein Folding", we introduced the concept of free energy and the protein folding landscape. Here, we provide a deeper, more formal underpinning of free energy in terms of the entropy and enthalpy; to this end, we will first need to better define the meaning of equilibrium, entropy and enthalpy. When we understand these concepts, we will come back for a more quantitative explanation of protein folding and dynamics. We will discuss the influence of temperature on the free energy landscape, and the difference between microstates and macrostates.

q-bio.BM↗