Analysis and Visualization of Protein Channels, Tunnels, and Pores with MOLEonline and ChannelsDB 2.0.

Channels, tunnels, and pores serve as pathways for the transport of molecules and ions through protein structures, thus participating to their functions. MOLEonline ( https://mole.upol.cz ) is an interactive web-based tool with enhanced capabilities for detecting and characterizing channels, tunnels, and pores within protein structures. MOLEonline has two distinct calculation modes for analysis of channel and tunnels or transmembrane pores. This application gives researchers rich analytical insights into channel detection, structural characterization, and physicochemical properties. ChannelsDB 2.0 ( https://channelsdb2.biodata.ceitec.cz/ ) is a comprehensive database that offers information on the location, geometry, and physicochemical characteristics of tunnels and pores within macromolecular structures deposited in Protein Data Bank and AlphaFill databases. These tunnels are sourced from manual deposition from literature and automatic detection using software tools MOLE and CAVER. MOLEonline and ChannelsDB visualization is powered by the LiteMol Viewer and Mol* viewer, ensuring a user-friendly workspace. This chapter provides an overview of user applications and usage.

ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era.

ChannelsDB 2.0 is an updated database providing structural information about the position, geometry and physicochemical properties of protein channels-tunnels and pores-within deposited biomacromolecular structures from PDB and AlphaFoldDB databases. The newly deposited information originated from several sources. Firstly, we included data calculated using a popular CAVER tool to complement the data obtained using original MOLE tool for detection and analysis of protein tunnels and pores. Secondly, we added tunnels starting from cofactors within the AlphaFill database to enlarge the scope of the database to protein models based on Uniprot. This has enlarged available channel annotations ∼4.6 times as of 1 September 2023. The database stores information about geometrical features, e.g. length and radius, and physico-chemical properties based on channel-lining amino acids. The stored data are interlinked with the available UniProt mutation annotation data. ChannelsDB 2.0 provides an excellent resource for deep analysis of the role of biomacromolecular tunnels and pores. The database is available free of charge: https://channelsdb2.biodata.ceitec.cz.

Data formats and standards for opportunistic rainfall sensors.

Opportunistic sensors are increasingly used for rainfall measurement. However, their raw data are collected by a variety of systems that are often not primarily intended for rainfall monitoring, resulting in a plethora of different data formats and a lack of common standards. This hinders the sharing of opportunistic sensing (OS) data, their automated processing, and, at the end, their practical usage and integration into standard observation systems. This paper summarises the experiences of the more than 100 members of the OpenSense Cost Action involved in the OS of rainfall. We review the current practice of collecting and storing precipitation OS data and corresponding metadata, and propose new common guidelines describing the requirements on data and metadata collection, harmonising naming conventions, and defining human-readable and machine readable file formats for data and metadata storage. We focus on three sensors identified by the OpenSense community as prominent representatives of the OS of precipitation: Commercial microwave links (CML): fixed point-to-point radio links mainly used as backhauling connections in telecommunication networks Satellite microwave links (SML): radio links between geostationary Earth orbit (GEO) satellites and ground user terminals. Personal weather stations (PWS): non-professional meteorological sensors owned by citizens. The conventions presented in this paper are primarily designed for storing, handling, and sharing historical time series and do not consider specific requirements for using OS data in real time for operational purposes. The conventions are already now accepted by the ever growing OpenSense community and represent an important step towards automated processing of OS raw data and community development of joint OS software packages.

Opportunistic sensors, devices primarily intended not intended for sensing, are increasingly used for rainfall measurement. The lack of conventions defining which data should be stored and how, makes it difficult to automatically process the data and integrate these observations into standard monitoring networks. This paper reviews current practice of collecting and storing precipitation opportunistic sensing (OS) data based on the experience of more than 100 members of the OpenSense Cost Action and suggest common data format standards. We focus on three sensors identified by the OpenSense community as prominent representatives of the OS of precipitation: Commercial microwave links (CML), Satellite Microwave Links (SML), and Personal Weather Stations (PWS). The conventions are already now accepted by the ever growing OpenSense community and represent an important step towards automated processing of OS raw data and community development of joint OS software packages.