Barbora Kozlikova

• PhD
• Professor (Associate) at Masaryk University

Virtual reality (VR) technology has become increasingly popular in education as a tool for enhancing learning experiences and engagement. This paper addresses the lack of a suitable tool for creating multi‐user immersive educational content for virtual environments by introducing a novel solution called eDIVE. The solution is designed to facilitate...

A large corpus of the literature related to BioMedical Visualization involves purely technical contributions without a specific application field in mind. This chapter focuses on an overview of the most commonly used techniques in BioMedVis and their evolution. We also include references to important surveys that cover each of the discussed topics...

In this chapter we discuss the research trends within individual application fields according to our taxonomy. Including all papers identified within our literature survey would not be feasible, and we, therefore, focus on the most influential works. The entire literature corpus and its categorization can be accessed and explored at the searchable...

In this book, we provided an overview of trends in biological and medical visualization from the early beginnings until now. To trace the evolution of the trends over the years

For a broader perspective on the evolution of the BioMedVis field, we contacted more than 50 researchers of mixed seniority and expertise, both from industry and academia and from all around the world. The intention was to have an overview of the status of the domain—not only from the point of published literature but also from the people forming t...

Effective security patrol management is critical for ensuring safety in diverse environments such as art galleries, airports, and factories. The behavior of patrols in these situations can be modeled by patrolling games. They simulate the behavior of the patrol and adversary in the building, which is modeled as a graph of interconnected nodes repre...

We apply an approach from cognitive linguistics by mapping Conceptual Metaphor Theory (CMT) to the visualization domain to address patterns of visual conceptual metaphors that are often used in science infographics. Metaphors play an essential part in visual communication and are frequently employed to explain complex concepts. However, their use i...

In understanding and redesigning the function of proteins in modern biochemistry, protein engineers are increasingly focusing on exploring regions in proteins called loops. Analyzing various characteristics of these regions helps the experts design the transfer of the desired function from one protein to another. This process is denoted as loop gra...

Getting acquainted with a large codebase can be a daunting task for software developers, both new and seasoned. The description of a codebase and its development should be the purpose of its documentation. However, software documentation, if it exists at all, is usually textual and accompanied only by simple static diagrams. It is also time-consumi...

In understanding and redesigning the function of proteins in modern biochemistry, protein engineers are increasingly focusing on exploring regions in proteins called loops. Analyzing various characteristics of these regions helps the experts design the transfer of the desired function from one protein to another. This process is denoted as loop gra...

Effective security patrol management is critical for ensuring safety in diverse environments such as art galleries, airports, and factories. The behavior of patrols in these situations can be modeled by patrolling games. They simulate the behavior of the patrol and adversary in the building, which is modeled as a graph of interconnected nodes repre...

We apply an approach from cognitive linguistics by mapping Conceptual Metaphor Theory (CMT) to the visualization domain to address patterns of visual conceptual metaphors that are often used in science infographics. Metaphors play an essential part in visual communication and are frequently employed to explain complex concepts. However, their use i...

The evolution and accumulation of snow cover are among the most important characteristics influencing Antarctica's climate and biotopes. The changes in Antarctica are also substantially impacting global climate change. Therefore, detailed monitoring of snow evolution is key to understanding such changes. One way to conduct this monitoring is by ins...

Molecular docking is a key technique in various fields like structural biology, medicinal chemistry, and biotechnology. It is widely used for virtual screening during drug discovery, computer-assisted drug design, and protein engineering. A general molecular docking process consists of the protein and ligand selection, their preparation, and the do...

The representations of biochemical processes must balance visual portrayals with descriptive content to be an effective learning tool. To determine what type of representation is the most suitable for education, we designed five different representations of adenosine triphosphate (ATP) synthesis and examined how they are perceived. Our representati...

Histopathology research quickly evolves thanks to advances in whole slide imaging (WSI) and artificial intelligence (AI). However, existing WSI viewers are tailored either for clinical or research environments, but none suits both. This hinders the adoption of new methods and communication between the researchers and clinicians. The paper presents...

Visualization plays a crucial role in molecular and structural biology. It has been successfully applied to a variety of tasks, including structural analysis and interactive drug design. While some of the challenges in this area can be overcome with more advanced visualization and interaction techniques, others are challenging primarily due to the...

We present ChromoSkein, a web-based tool for visualizing three-dimensional chromatin models. The spatial organization of chromatin is essential to its function. Experimental methods, namely Hi-C, reveal the spatial conformation but output a 2D matrix representation. Biologists leverage simulation to bring this information back to 3D, assembling a 3...

We present sMolBoxes, a dataflow representation for the exploration and analysis of long molecular dynamics (MD) simulations. When MD simulations reach millions of snapshots, a frame-by-frame observation is not feasible anymore. Thus, biochemists rely to a large extent only on quantitative analysis of geometric and physico-chemical properties. Howe...

We present sMolBoxes, a dataflow representation for the exploration and analysis of long molecular dynamics (MD) simulations. When MD simulations reach millions of snapshots, a frame-by-frame observation is not feasible anymore. Thus, biochemists rely to a large extent only on quantitative analysis of geometric and physico-chemical properties. Howe...

The transplantation of loops between structurally related proteins is a compelling method to improve the activity, specificity and stability of enzymes. However, despite the interest of loop regions in protein engineering, the available methods of loop-based rational protein design are scarce. One particular difficulty related to loop engineering i...

In the process of understanding and redesigning the function of proteins in modern biochemistry, protein engineers are increasingly focusing on the exploration of regions in proteins called loops. Analyzing various characteristics of these regions helps the experts to design the transfer of the desired function from one protein to another. This pro...

DNA nanostructures offer promising applications, particularly in the biomedical domain, as they can be used for targeted drug delivery, construction of nanorobots, or as a basis for molecular motors. One of the most prominent techniques for assembling these structures is DNA origami. Nowadays, desktop applications are used for the in silico design...

Educational videos are traditional means of communicating scientific findings to a broader audience. Nowadays, they are also a very common medium in distant teaching. However, creating videos using the existing software tools can be very challenging for inexperienced users. Also, the student’s engagement in standard videos is often very limited as...

High-dimensional configuration space is usually searched using sampling-based motion planning methods. The well-known issue of sampling-based planners is the narrow passage problem caused by small regions of the configuration space that are difficult to cover by random samples. Practically, the presence of narrow passages decreases the probability...

In the modern drug discovery process, medicinal chemists deal with the complexity of analysis of large ensembles of candidate molecules. Computational tools, such as dimensionality reduction (DR) and classification, are commonly used to efficiently process the multidimensional space of features. These underlying calculations often hinder interpreta...

The daily routine of criminal investigators consists of a thorough analysis of highly complex and heterogeneous data of crime cases. Such data can consist of case descriptions, testimonies, criminal networks, spatial and temporal information, and virtually any other data that is relevant for the case. Criminal investigators work under heavy time pr...

In the modern drug discovery process, medicinal chemists deal with the complexity of analysis of large ensembles of candidate molecules. Computational tools, such as dimensionality reduction (DR) and classification, are commonly used to efficiently process the multidimensional space of features. These underlying calculations often hinder interpreta...

Proteins perform a large variety of functions in living organisms, thus playing a key role in biology. As of now, available learning algorithms to process protein data do not consider several particularities of such data and/or do not scale well for large protein conformations. To fill this gap, we propose two new learning operations enabling deep...

Computation of trajectories for ligand binding and unbinding via protein tunnels and channels is important for predicting possible protein–ligand interactions. These highly complex processes can be simulated by several software tools, which provide biochemists with valuable information for drug design or protein engineering applications. This paper...

Visualization has evolved into a mature scientific field and it has also become widely accepted as a standard approach in diverse fields, including physics, life sciences, and business intelligence. However, despite its successful development, there are still many open research questions that require customized implementations in order to explore a...

We present a method for the browsing of hierarchical 3D models in which we combine the typical navigation of hierarchical structures in a 2D environment---using clicks on nodes, links, or icons---with a 3D spatial data visualization. Our approach is motivated by large molecular models, for which the traditional single-scale navigational metaphors a...

Networks of protein–protein interactions (PPI) constitute either stable or transient complexes in every cell. Most of the cellular complexes keep their function, and therefore stay similar, during evolution. The evolutionary constraints preserve most cellular functions via preservation of protein structures and interactions. The evolutionary conser...

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...

Analyzing molecular dynamics (MD) simulations is a key aspect to understand protein dynamics and function. With increasing computational power, it is now possible to generate very long and complex simulations, which are cumbersome to explore using traditional 3D animations of protein movements. Guided by requirements derived from multiple focus gro...

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...

Proteins are involved in many biochemical processes. The behavior of proteins is highly influenced by the presence of internal void space, in literature denoted as tunnels or cavities. Tunnels are paths leading from an inner protein active site to its surface. The knowledge about tunnels and their evolution over time, captured in molecular dynamics...

Labeling is intrinsically important for exploring and understanding complex environments and models in a variety of domains. We present a method for interactive labeling of crowded 3D scenes containing very many instances of objects spanning multiple scales in size. In contrast to previous labeling methods, we target cases where many instances of d...

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 fol...

Motivation Studying the transport paths of ligands, solvents, or ions in transmembrane proteins and proteins with buried binding sites is fundamental to the understanding of their biological function. A detailed analysis of the structural features influencing the transport paths is also important for engineering proteins for biomedical and biotechn...

Background: Studying the patterns of protein-protein interactions (PPIs) is fundamental for understanding the structure and function of protein complexes. The exploration of the vast space of possible mutual configurations of interacting proteins and their contact zones is very time consuming and requires the proteomic expert knowledge. Results:...

Protein tunnels connecting the functional buried cavities with bulk solvent and protein channels, enabling the transport through biological membranes, represent the structural features that govern the exchange rates of ligands, ions, and water solvent. Tunnels and channels are present in a vast number of known proteins and provide control over thei...

We present the first approach to integrative structural modeling of the biological mesoscale within an interactive visual environment. These complex models can comprise up to millions of molecules with defined atomic structures, locations, and interactions. Their construction has previously been attempted only within a non-visual and non-interactiv...

Digital approaches to shape comparison and analysis play a very important role in forensic anthropology. New methods are still emerging and the whole area is experiencing a shift from traditional 2D image data to processing of 3D meshes. Therefore, the visual exploration of 3D meshes and methods for their visual comparison play a crucial role in th...

Generating large human crowds of distinguishable individuals is one of the challenges in the gaming industry. When the scene contains many characters, it becomes impracticable to create all the individual characters manually. However, the requirement for the different appearances of individuals in a crowd, namely their faces, is now in greater dema...

Background Protein function is determined by many factors, namely by its constitution, spatial arrangement, and dynamic behavior. Studying these factors helps the biochemists and biologists to better understand the protein behavior and to design proteins with modified properties. One of the most common approaches to these studies is to compare the...

Background Protein structures and their interaction with ligands have been in the focus of biochemistry and structural biology research for decades. The transportation of ligand into the protein active site is often complex process, driven by geometric and physico-chemical properties, which renders the ligand path full of jitter and impasses. This...

Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of thre...

In this report we review and structure the branch of molecular visualization that is concerned with the visual analysis of cavities in macromolecular protein structures. First the necessary background, the domain terminology, and the goals of analytical reasoning are introduced. Based on a comprehensive collection of relevant research works, we pre...

The reactivity of the biomolecular structures is highly influenced by their structural features. Thus, studying these features along with the exploration of their dynamic behavior helps to understand the processes ongoing in living cells. This can be reached by the visual representation of these processes as visualization is one of the most natural...

In this paper we propose a novel method for the interactive exploration of protein tunnels. The basic principle of our approach is that we entirely abstract from the 3D/4D space the simulated phenomenon is embedded in. A complex 3D structure and its curvature information is represented only by a straightened tunnel centerline and its width profile....

Generating human faces is an important task in many research and application fields, including the gaming industry. When the scene contains many characters, it becomes impracticable to create all individual characters manually. On the other hand, the requirement for the different appearance of faces of individuals in a crowd is now more in demand....

This paper summarizes the results of an experiment performed as basic research of 3D display of geographical information using with two alternative control devices (a Wii Remote Controller and a mouse). The aim was to explore the influence of a specific type of visualization on the human understanding of depicted geographical information and to dis...

Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of thre...

Studying the characteristics of proteins and their inner void space, including their geometry, physico-chemical properties and dynamics are instrumental for evaluating the reactivity of the protein with other small molecules. The analysis of long simulations of molecular dynamics produces a large number of voids which have to be further explored an...

We present a simple and fast path planning algorithm for transportation of a set of tightly connected sphere objects (a small molecule) through a narrow gap. In our approach we are using common sampling-based path planning, however, instead of sampling the entire configuration space, we estimate which subsets of this space must be crossed on the de...

Structural properties of proteins substantially influence their reactivity. Thus, the presence of pathways serving for transportation of a small molecule to the protein active site is crucial. These pathways, called tunnels, are defined by their surroundings --- tunnel lining amino acids (or residues). In consequence, studying these amino acids and...

Abstrakt NEWRON je terapeutický software, který je zaměřen na podporu a rozvoj lidí s různými psycho-sociálními obtížemi. Aplikace sestává ze sady her, které aktivně působí na sociální vnímání a sociální interakce uživatelů, aktivuje jejich kognitivní, psychomotorické či rozhodovací funkce a současně posiluje efektivní využívání moderních informačn...

The biological function of a macromolecule often requires that a small molecule or ion is transported through its structure. The transport pathway often leads through void spaces in the structure. The properties of transport pathways change significantly in time; therefore, the analysis of a trajectory from molecular dynamics rather than of a singl...

The transport of ligands, ions or solvent molecules into proteins with buried binding sites or through the membrane is enabled by protein tunnels and channels. CAVER Analyst is a software tool for calculation, analysis and real-time visualization of access tunnels and channels in static and dynamic protein structures. It provides an intuitive graph...

Proteins are essential for functioning of all living organisms and studying their inner structure and functions has been of a high importance. Many studies concentrated on detection of various inner structures inside macromolecules (e.g. tunnels, channels, pores) which play an essential role in the functioning of a large number of proteins. Here we...

Long-term research in the area of protein analysis proved the importance of an empty space situated inside these macromolecular structures. This empty space influences the protein function, characteristics or reactivity. Many algorithms enabling computation of these empty spaces (or voids) have been published and their results were evaluated by pro...

Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins. Characteristics of individual transport pathways, including their geometry, physico-chemical properties and dynamics are instrumental for understanding of structure-function relationships of these proteins, for the design of new...

Analysis of crystal structures of DhaA. (PDF)

Comparison of pathways calculated by CAVER 3.0, MOLE 1.2 and MolAxis 1.4. (PDF)

Comparison of characteristics of the DhaA p1 tunnel obtained by the analysis of the molecular dynamics trajectory and crystal structures. (PDF)

Clusters of pathways calculated in the molecular dynamics simulation of haloalkane dehalogenase DhaA by CAVER 3.0 (A–C) and MOLE 1.2 (D–F). Pathways identified throughout the simulation are shown in one frame as pathway centerlines; if more pathways from the same snapshot are grouped to the same cluster, only the pathway with the lowest cost is sho...

Comparison of CAVER 3.0, MOLE 1.2 and MolAxis 1.4. (PDF)

Bottleneck residues of the top ranked tunnels of DhaA identified by CAVER 3.0 in molecular dynamics trajectory using the probe radius of 0.9 Å and the clustering threshold of 3.5. (PDF)

Molecular dynamics simulation of haloalkane dehalogenase DhaA. (PDF)

Analysis of molecular dynamics simulation of DhaA. (PDF)

Characteristics of the pathways identified in 10,000 snapshots of the 10 ns molecular dynamics trajectory of DhaA using the probe radius of 0.9 Å and the clustering threshold of 4.3. (PDF)

Characteristics of the pathways identified in DhaA crystal structures using the probe radius of 0.8 Å. (PDF)

Evaluation of potential false positive results. (PDF)

Comparison of tunnels identified by CAVER 3.0 with known DhaA tunnels. (PDF)

Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins. Characteristics of individual transport pathways, including their geometry, physico-chemical properties and dynamics are instrumental for understanding of structure-function relationships of these proteins, for the design of new...

Visualization of molecular structures and their character-istics represents a very popular and extensive area of com-puter graphics, in which the researchers are intensively interested for the last decades. During this time there have been developed many methods for visualization of molecules, which are trying to satisfy the needs of bio-chemists....

This paper presents two novel techniques for visualization of tunnels in complex molecules of proteins. Long-term research in the field of protein analysis proved that the reactivity of the protein molecule depends on the presence of tunnels. These structures are very important mainly in the process of finding new pharmaceuticals. Visualization of...