生物化学技术

In the past decade macromolecular crystallography has undergone major advances in crystallization, data collection by synchrotron X-ray sources and area detectors, and data analysis by high performance computers and new computational techniques. In addition, recombinant g ...

Crystallographic models are built by interpretation of an experimental image, the electron density map. This map is generally calculated from amplitudes measured experimentally and phases obtained with the multiple isomorphous replacement method. This method has poor preci ...

Refinement constitutes the last of the three main steps in the crystallographic establishment of a molecular structure, which are fast, crystal growth and data collection; second, phase determination and calculation of electron density maps; and third, model building and refinemen ...

Mathematical models of biological processes become more and more important in biology. The aim is a holistic understanding of how processes such as cellular communication, cell division, regulation, homeostasis, or adaptation work, how they are regulated, and how they react to perturb ...

Recent observational techniques based upon confocal microscopy make it possible to observe cells at a scale that has never been probed before: the mesoscopic scale. In the eukaryotic cell nucleus, many objects demonstrating phenomena occurring at this scale, such as nuclear bodies, are c ...

Computational methods for predicting protein interaction partners are becoming increasingly popular. Many of them are mature enough to be widely used by molecular biologists who can look for proteins related to the protein of interest in order to infer information about its context in the ...

Prism (protein interactions by structural matching) is a system that employs a novel prediction algorithm for protein–protein interactions. It adopts a bottom-up approach that combines structure and sequence conservation in protein interfaces. The algorithm seeks possible b ...

Structural designability is the number of ways it is possible to encode for structure. A protein’s designability has been equated with the size of sequence space encoding for the protein’s structure, a measure that reflects the structure’s robustness to mutation. Current evidence sugges ...

Genome sequencing projects have resulted in a rapid accumulation of predicted protein sequences. With experimentally verified information on protein function lagging far behind, computational methods are used for functional annotation of proteins. Here we describe a number of ...

Proteins perform many important tasks in living organisms, such as catalysis of biochemical reactions, transport of nutrients, and recognition and transmission of signals. The plethora of aspects of the role of any particular protein is referred to as its “function.” One aspect of protein f ...

Biomedical knowledge is to a very large extent represented only in textual form. To make this knowledge accessible to humans and/or further automatic processing, text mining applications have been developed. At the end of this chapter we present an overview of the most important open access ap ...

Protein sequence alignment is the task of identifying evolutionarily or structurally related positions in a collection of amino acid sequences. Although the protein alignment problem has been studied for several decades, many recent studies have demonstrated considerable pro ...

With genome sequencing projects producing huge amounts of sequence data, database sequence similarity search has become a central tool in bioinformatics to identify potentially homologous sequences. It is thus widely used as an initial step for sequence characterization and anno ...

MassSorter is a software tool that sorts, systemizes, and analyzes data from peptide mass fingerprinting (PMF) experiments on proteins with known amino acid sequences. Several experiments can be simultaneously analyzed for sequence coverage and posttranslational modificat ...

One fundamental problem in proteomics study is to identify proteins and determine their expression levels in cells. Coupled with advanced liquid chromatography, tandem mass spectrometry has become the standard tool for peptide sequencing. In the past decade, many different algori ...

Driven by advances in mass spectrometry and analytical chemistry, coupled with the expanding number of completely sequenced genomes, proteomics is becoming a widely exploited technology for characterizing the proteins found in living systems. As proteomics becomes increasi ...

Many fundamental processes involve protein–protein interactions. Recent advances in technology make it possible to perform large–scale, genome–wide interaction mapping experiments that result in an always increasing amount of data. Protein–protein interaction datab ...

The PRIDE database has been developed to allow the proteomics community to share publicly, or within private collaborations, the vast volume of data generated by proteomics laboratories across the globe. These data are being generated at an expanding rate as increasingly sophisticat ...

Proteomics data can be diverse and complex, and are typically produced on a large scale. To allow sharing and centralized storage and dissemination of such results, the Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has created a set of community standards for t ...

Prefractionation of complex protein samples prior to mass spectrometry provides a method for the isolation of low-abundance proteins into specific fractions thereby enabling their identification. Free-flow electrophoresis in the isoelectric focusing mode (IEF-FFE) pre ...