Chemical cross-linking mass spectrometry has become a popular tool in structural biology. Although several algorithms exist that efficiently analyze data-dependent mass spectrometric data, the algorithm to identify and quantify intermolecular cross-links located at the interaction interface of homodimer molecules was missing. The algorithm in LinX utilizes high mass accuracy for ion identification. In contrast with standard data-dependent analysis, LinX enables the elucidation of cross-linked peptides originating from the interaction interface of homodimers labeled by 14N/15N, including their ratio or cross-links from protein-nucleic acid complexes. The software is written in Java language, and its source code and a detailed user's guide are freely available at https://github.com/KukackaZ/LinX or https://ms-utils.org/LinX. Data are accessible via the ProteomeXchange server with the data set identifier PXD023522.

• Keywords
• chemical cross-linking, data interpretation, high resolution, homo oligomers, mass spectrometry, nucleic acids, proteins,
• MeSH
• Algorithms MeSH
• Mass Spectrometry MeSH
• Peptides * MeSH
• Cross-Linking Reagents MeSH
• Software * MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Peptides * MeSH
• Cross-Linking Reagents MeSH

Skin and membrane permeation experiments comprise an important step in the development of a transdermal or topical formulation or toxicological risk assessment. The standard method for analyzing these data relies on the linear part of a permeation profile. However, it is difficult to objectively determine when the profile becomes linear, or the experiment duration may be insufficient to reach a maximum or steady state. Here, we present a software tool for Skin And Membrane Permeation data Analysis, SAMPA, that is easy to use and overcomes several of these difficulties. The SAMPA method and software have been validated on in vitro and in vivo permeation data on human, pig and rat skin and model stratum corneum lipid membranes using compounds that range from highly lipophilic polycyclic aromatic hydrocarbons to highly hydrophilic antiviral drug, with and without two permeation enhancers. The SAMPA performance was compared with the standard method using a linear part of the permeation profile and a complex mathematical model. SAMPA is a user-friendly, open-source software tool for analyzing the data obtained from skin and membrane permeation experiments. It runs on a Microsoft Windows platform and is freely available as a Supporting file to this article.

• Keywords
• Data analysis, Flux, Skin permeability, Software, Transdermal drug delivery,
• MeSH
• Skin Absorption * MeSH
• Rats MeSH
• Skin metabolism   MeSH
• Pharmaceutical Preparations metabolism   MeSH
• Humans MeSH
• Cell Membrane Permeability MeSH
• Swine MeSH
• Software * MeSH
• Animals MeSH
• Check Tag
• Rats MeSH
• Humans MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Pharmaceutical Preparations MeSH

This article briefly describes the development of the I-COP tool, which is designed to promote education and decision making of clinical oncologists. It is based on real data from medical facilities, which are processed, stored in database, analyzed and finally displayed in an interactive software application. Used data sources are shortly described in individual sections together with the functionality of developed tools. The final goal of this project is to provide support for work and education within each involved partner center. Clinical oncologists are therefore supposed to be the authors and users at the same time.

• MeSH
• Algorithms MeSH
• Data Mining methods   MeSH
• Electronic Health Records * MeSH
• Humans MeSH
• Decision Support Techniques MeSH
• Neoplasms diagnosis   therapy   MeSH
• Software Design MeSH
• Registries * MeSH
• Software * MeSH
• Decision Support Systems, Clinical * MeSH
• Health Records, Personal * MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Geographicals
• Czech Republic MeSH

The paper gives an objective sight on extent variety of submitted statistical packages. It's especially evaluated range and quality of statistical methods, user environment and graphical facility of software. The paper brings information which is dispersed in many sources and therefore is hardly accessible.

• MeSH
• Software * MeSH
• Statistics as Topic * MeSH
• Publication type
• English Abstract MeSH
• Journal Article MeSH

The authors give an account of different types of commercially supplied programmes which can be used also in the health services. They discuss the properties and types of different software - data base programmes, text processors, graphic and statistical programmes and finally so-called integrated software along with data on possible mutual combinations. At the same time also general conditions for the application of these programmes within the framework of clinical informations systems are discussed incl. their advantages and short-comings.

• MeSH
• Medical Informatics * MeSH
• Software * MeSH
• Publication type
• English Abstract MeSH
• Journal Article MeSH

Super-resolution optical fluctuation imaging (SOFI) allows one to perform sub-diffraction fluorescence microscopy of living cells. By analyzing the acquired image sequence with an advanced correlation method, i.e. a high-order cross-cumulant analysis, super-resolution in all three spatial dimensions can be achieved. Here we introduce a software tool for a simple qualitative comparison of SOFI images under simulated conditions considering parameters of the microscope setup and essential properties of the biological sample. This tool incorporates SOFI and STORM algorithms, displays and describes the SOFI image processing steps in a tutorial-like fashion. Fast testing of various parameters simplifies the parameter optimization prior to experimental work. The performance of the simulation tool is demonstrated by comparing simulated results with experimentally acquired data.

• MeSH
• Algorithms MeSH
• Microscopy, Fluorescence * MeSH
• HeLa Cells MeSH
• Humans MeSH
• Image Processing, Computer-Assisted methods   MeSH
• Software * MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH

BACKGROUND: Visualization of RNA secondary structures is a complex task, and, especially in the case of large RNA structures where the expected layout is largely habitual, the existing visualization tools often fail to produce suitable visualizations. This led us to the idea to use existing layouts as templates for the visualization of new RNAs similarly to how templates are used in homology-based structure prediction. RESULTS: This article introduces Traveler, a software tool enabling visualization of a target RNA secondary structure using an existing layout of a sufficiently similar RNA structure as a template. Traveler is based on an algorithm which converts the target and template structures into corresponding tree representations and utilizes tree edit distance coupled with layout modification operations to transform the template layout into the target one. Traveler thus accepts a pair of secondary structures and a template layout and outputs a layout for the target structure. CONCLUSIONS: Traveler is a command-line open source tool able to quickly generate layouts for even the largest RNA structures in the presence of a sufficiently similar layout. It is available at http://github.com/davidhoksza/traveler .

• Keywords
• RNA secondary structure, Software tool, Template-based modeling, Visualization,
• MeSH
• Algorithms MeSH
• Nucleic Acid Conformation MeSH
• RNA chemistry   MeSH
• Software * MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• RNA MeSH

Protein structures contain highly complex systems of voids, making up specific features such as surface clefts or grooves, pockets, protrusions, cavities, pores or channels, and tunnels. Many of them are essential for the migration of solvents, ions and small molecules through proteins, and their binding to the functional sites. Analysis of these structural features is very important for understanding of structure-function relationships, for the design of potential inhibitors or proteins with improved functional properties. Here we critically review existing software tools specialized in rapid identification, visualization, analysis and design of protein tunnels and channels. The strengths and weaknesses of individual tools are reported together with examples of their applications for the analysis and engineering of various biological systems. This review can assist users with selecting a proper software tool for study of their biological problem as well as highlighting possible avenues for further development of existing tools. Development of novel descriptors representing not only geometry, but also electrostatics, hydrophobicity or dynamics, is needed for reliable identification of biologically relevant tunnels and channels.

• MeSH
• Protein Conformation MeSH
• Models, Molecular * MeSH
• Proteins chemistry   metabolism   MeSH
• Software * MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Review MeSH
• Names of Substances
• Proteins MeSH

The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world.

• Keywords
• CCP4, Collaborative Computational Project No. 4, crystallography software, macromolecular crystallography,
• MeSH
• Crystallography, X-Ray MeSH
• Macromolecular Substances MeSH
• Proteins * chemistry   MeSH
• Software * MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Macromolecular Substances MeSH
• Proteins * MeSH

Progress in mass spectrometry lipidomics has led to a rapid proliferation of studies across biology and biomedicine. These generate extremely large raw datasets requiring sophisticated solutions to support automated data processing. To address this, numerous software tools have been developed and tailored for specific tasks. However, for researchers, deciding which approach best suits their application relies on ad hoc testing, which is inefficient and time consuming. Here we first review the data processing pipeline, summarizing the scope of available tools. Next, to support researchers, LIPID MAPS provides an interactive online portal listing open-access tools with a graphical user interface. This guides users towards appropriate solutions within major areas in data processing, including (1) lipid-oriented databases, (2) mass spectrometry data repositories, (3) analysis of targeted lipidomics datasets, (4) lipid identification and (5) quantification from untargeted lipidomics datasets, (6) statistical analysis and visualization, and (7) data integration solutions. Detailed descriptions of functions and requirements are provided to guide customized data analysis workflows.

• MeSH
• Informatics MeSH
• Lipidomics * MeSH
• Lipids chemistry   MeSH
• Software MeSH
• Computational Biology * methods   MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Review MeSH
• Research Support, N.I.H., Extramural MeSH
• Names of Substances
• Lipids MeSH