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Documentation

RINalyzer Documentation


RINerator Documentation



New Features

  • Interface to UCSF Chimera
    The new interface to UCSF Chimera is implemented in the structureViz app and basically runs in the background. structureViz keeps track of open structures and automatically associates them with the corresponding networks, nodes and edges in Cytoscape if and only if the nodes are correctly annotated. The required attributes are generated automatically for each RIN if any of the three methods for importing and generating RINs described below is used. See an extended description here.

  • Import and generation of RINs
    • Import RIN from Web Service
      This feature allows the direct retrieval of RIN data from our web service RINdata. It automatically imports the RIN and the associated attributes as well as opens the corresponding PDB structure in UCSF Chimera. Since the protein structure cannot be saved in Cytoscape, it is saved for further use into USER_HOME/CytoscapeConfigureation/pdbs/.
    • Import RIN from File
      This option should be used to import any RIN, which is supported so far by RINalyzer or follows these specifications). In this way, the attribute data required for associating the RIN with a protein structure in UCSF Chimera is generated automatically.
    • Create RIN from Chimera
      The completely new functionality to generate RINs from a selection of residues in UCSF Chimera is implemented in the structureViz app and can be invoked from RINalyzer as well. The selection can include amino acid residues, solvent molecules, ligands, etc. Currently, five types of edges can be created: contacts, clashes, hydrogen bonds, connectivity (backbone), and Cα distances. See also the structureViz app webpage for more details.

  • RIN Layout
    This layout is specifically implemented for RINs and synchronizes orientation and location between a RIN and the corresponding structure. It automatically retrieves the current 3D coordinates of the residues and uses their projection on a 2D plane as a starting point for a distance-based stress minimization layout.

  • Annotation of RINs
    The RINalyzer and structureViz apps can transfer residue attributes from UCSF Chimera as node attributes to the corresponding RIN in Cytoscape. In particular, these attributes include secondary structure, residue coordinates, hydrophobicity, solvent accessible surface area (if already computed in UCSF Chimera), occupancy, etc. See also the structureViz app webpage for more details.

  • Exploration of RINs
    • Extract Interfaces
      In addition to creating a new network for a single or multiple chains in a RIN, RINalyzer can extract a new subnetwork consisting of the interface residues and their interactions between two or more chains. Interface residues are defined as residues with at least one non-covalent interaction to a residue in another chain. This option can be found in the RINalyzer menu Extract Subnetwork.
    • Create Aggregated RIN
      This feature invokes the generation of an aggregated network, in which a node represents a group of consecutive residues with the same characteristic, for example, protein chain, domain, or secondary structure element.
    • Edge Distance Filter
      This option is included in the RIN Visual Properties dialog and allows hiding edges between residues closer in sequence than the specified threshold.

  • Comparison of RINs
    The comparison functionality of RINalyzer has been greatly improved and linked to the structure alignment tool of UCSF Chimera, i.e., two RINs can be compared based on the sequence or structure alignment of their associated protein structures. Alternatively, the mapping of nodes can be provided as a FASTA alignment file or a simple node-to-node text mapping file. In addition, the difference of edge weights (represented by a numeric edge attribute with the same name in both RINs) can be computed and mapped to the edges in the comparison network. See more documentation here.

  • Node and edge sets
    The node sets functionality of RINalyzer has been replaced by a new app called setsApp, which is available for download from the Cytoscape App Store. In addition to sets of nodes, it also supports various operations on sets of edges. For more documentation, see here.



RINalyzer App Menus

  • RINdata Web Service Client
    Import a RIN for a user-specified PDB identifier from RINdata. The corresponding edge attributes and protein structure are also imported. See more documentation here.

  • Import RIN from File
    Import a RIN as supported so far by RINalyzer (see RIN Specification). See more documentation here.

  • RIN Visual Properties
    Hide edges by type or distance and change the appearance of a RIN by mapping some node or edge attributes to visual properties of the network. See more documentation here.

  • Open Structure from File
    Open a protein structure file provided by the user for the current RIN (the structureViz app should be installed). See more documentation here.

  • Open Protein Structure
    Open a protein structure associated with an arbitrary node in the current RIN (the structureViz app should be installed). See more documentation here.

  • Close Protein Structure
    Close a protein structure associated with an arbitrary node in the current RIN (the structureViz app should be installed). See more documentation here.

  • Create RIN from Chimera
    Create a RIN from a current selection in UCSF Chimera (the structureViz app should be installed). See more documentation here.

  • Annotate RIN from Chimera
    Annotate the current RIN with structural information from a currently open and associated protein structure in UCSF Chimera (the structureViz app should be installed). See more documentation here.

  • Sync RIN Colors with Chimera
    Synchronize node and residue colors between the current RIN and its associated protein structure (the structureViz app should be installed). See more documentation here.

  • Analyze Network
    Compute weighted centrality measures with respect to a set of selected nodes. See more documentation here.

  • Extract Subnetwork
    Create a new network containing the nodes and interactions within or between user-specified protein chain(s). See more documentation here.

  • Create Aggregated RIN
    Create an aggregated RIN based on a property such as secondary structure. See more documentation here.

  • Compare RINs
    Compare two RINs based on a structure alignment of the corresponding 3D protein structures. See more documentation here.

  • About
    Show the About box of RINalyzer including contributors and reference for citation.