text: When studying multi-body protein complexes, biochemists use computational tools that can suggest hundreds or thousands of their possible spatial configurations. However, it is not feasible to experimentally verify more than only a very small subset of them. In this paper, we propose a novel multiscale visual drilldown approach that was designed in tight collaboration with proteomic experts, enabling a systematic exploration of the configuration space. Our approach takes advantage of the hierarchical structure of the data -- from the whole ensemble of protein complex configurations to the individual configurations, their contact interfaces, and the interacting amino acids. Our new solution is based on interactively linked 2D and 3D views for individual hierarchy levels and at each level, we offer a set of selection and filtering operations enabling the user to narrow down the number of configurations that need to be manually scrutinized. Furthermore, we offer a dedicated filter interface, which provides the users with an overview of the applied filtering operations and enables them to examine their impact on the explored ensemble. This way, we maintain the history of the exploration process and thus enable the user to return to an earlier point of the exploration. We demonstrate the effectiveness of our approach on two case studies conducted by collaborating proteomic experts.
  @cite_1: Background The development of accurate protein-protein docking programs is making this kind of simulations an effective tool to predict the 3D structure and the surface of interaction between the molecular partners in macromolecular complexes. However, correctly scoring multiple docking solutions is still an open problem. As a consequence, the accurate and tedious screening of many docking models is usually required in the analysis step.
  @cite_25: 
  @cite_22: Summary: Herein we present COCOMAPS, a novel tool for analyzing, visualizing and comparing the interface in protein-protein and protein-nucleic acids complexes. COCOMAPS combines traditional analyses and 3D visualization of the interface with the effectiveness of intermolecular contact maps. Availability: COCOMAPS is accessible as a public web tool at http: www.molnac.unisa.it BioTools cocomaps
  @cite_6: Abstract We provide a high-level survey of multiscale molecular visualization techniques, with a focus on application-domain questions, challenges, and tasks. We provide a general introduction to molecular visualization basics and describe a number of domain-specific tasks that drive this work. These tasks, in turn, serve as the general structure of the following survey. First, we discuss methods that support the visual analysis of molecular dynamics simulations. We discuss, in particular, visual abstraction and temporal aggregation. In the second part, we survey multiscale approaches that support the design, analysis, and manipulation of DNA nanostructures and related concepts for abstraction, scale transition, scale-dependent modeling, and navigation of the resulting abstraction spaces. In the third part of the survey, we showcase approaches that support interactive exploration within large structural biology assemblies up to the size of bacterial cells. We describe fundamental rendering techniques as well as approaches for element instantiation, visibility management, visual guidance, camera control, and support of depth perception. We close the survey with a brief listing of important tools that implement many of the discussed approaches and a conclusion that provides some research challenges in the field.
summary: Although these schematic representations are conveying the information about a single configuration, they do not support the comparison and interactive filtering of entire ensembles of configurations. This issue is addressed in the CoCoMaps @cite_22 and COZOID @cite_25 tools. Both tools come with linked visualizations, aiding the users in analyzing and comparing interactions between protein pairs. CoCoMaps and its successor CONS-COCOMAPS @cite_1 enable to measure and visualize the consensus in multiple docking solutions and display the conservation of residue contacts using intermolecular contact maps. The COZOID tool uses a set of linked views for the interactive exploration of large ensembles of protein pairs, supporting a visual drilldown approach for narrowing down the set of possibly relevant configurations. The main limitation of these approaches is that they are operating only on protein pairs (i.e., single ) and cannot be directly applied to multi-body complexes. The multiscale aspect in molecular visualization can be explored on different granularity levels, as shown in the recent survey of @cite_6 .