A guide to the visual analysis and communication of biomolecular structural data

A comprehensive review on structural insights through molecular visualization: tools, applications, and limitations

CONTEXT

Biomolecules serve as intrinsic repositories of information related to function, binding interactions, molecular motion, and structural conformations. With the rapid accumulation of structural data from fields such as structural biology and cheminformatics, the ability to visualize biomolecular architecture has become essential for researchers in biology, pharmacology, and related disciplines. Molecular visualization represents a foundational step in accessing and interpreting this data, enabling its application in diverse scientific and therapeutic contexts. Recent advancements in computational algorithms and web-based visualization platforms have provided powerful resources for structural biologists, chemists, and crystallographers, facilitating efficient analysis and reproducibility of experimental outcomes. This review offers a comprehensive overview of contemporary molecular visualization tools, emphasizing their practical applications. Particular attention is given to PyMOL and NGL Viewer, with detailed guidance for their implementation in visualizing proteins, DNA, protein-ligand complexes, protein-protein interactions, protein-DNA assemblies, and small molecule ligands. Challenges frequently encountered in structural biology and cheminformatics, such as the identification of lead compounds for therapeutic development, are also addressed. Molecular dynamics simulations, including binding free energy calculations, are discussed as cost- and time-effective strategies to enhance drug discovery pipelines. In response to the increasing complexity of data-driven research, this review aims to serve as a valuable resource for professionals seeking efficient, reliable visualization tools to support structure-based research and drug design.

METHODS

This review article provides a comprehensive comparative analysis of biomolecular visualization features integrated into standalone and web-based molecular visualization tools. PyMOL (standalone) and NGL (web-based) were systematically employed to visualize proteins, ligands, protein-ligand complexes, protein-protein complexes, and protein-DNA complexes. The methodological framework outlined in this study establishes standardized guidelines for the effective utilization of molecular visualization tools, offering valuable insights for structural biologists and researchers engaged in molecular modeling and structural analysis.

Design principles for molecular animation

Molecular visualization is a powerful way to represent the complex structure of molecules and their higher order assemblies, as well as the dynamics of their interactions. Although conventions for depicting static molecular structures and complexes are now well established and guide the viewer's attention to specific aspects of structure and function, little attention and design classification has been devoted to how molecular motion is depicted. As we continue to probe and discover how molecules move - including their internal flexibility, conformational changes and dynamic associations with binding partners and environments - we are faced with difficult design challenges that are relevant to molecular visualizations both for the scientific community and students of cell and molecular biology. To facilitate these design decisions, we have identified twelve molecular animation design principles that are important to consider when creating molecular animations. Many of these principles pertain to misconceptions that students have primarily regarding the agency of molecules, while others are derived from visual treatments frequently observed in molecular animations that may promote misconceptions. For each principle, we have created a pair of molecular animations that exemplify the principle by depicting the same content in the presence and absence of that design approach. Although not intended to be prescriptive, we hope this set of design principles can be used by the scientific, education, and scientific visualization communities to facilitate and improve the pedagogical effectiveness of molecular animation.

A Concise Review of Biomolecule Visualization

The structural characteristics of biomolecules are a major focus in the field of structural biology. Molecular visualization plays a crucial role in displaying structural information in an intuitive manner, aiding in the understanding of molecular properties. This paper provides a comprehensive overview of core concepts, key techniques, and tools in molecular visualization. Additionally, it presents the latest research findings to uncover emerging trends and highlights the challenges and potential directions for the development of the field.

Changing Aesthetics in Biomolecular Graphics

Aesthetics for the visualization of biomolecular structures have evolved over the years according to technological advances, user needs, and modes of dissemination. In this article, we explore the goals, challenges, and solutions that have shaped the current landscape of biomolecular imagery from the overlapping perspectives of computer science, structural biology, and biomedical illustration. We discuss changing approaches to rendering, color, human-computer interface, and narrative in the development and presentation of biomolecular graphics. With this historical perspective on the evolving styles and trends in each of these areas, we identify opportunities and challenges for future aesthetics in biomolecular graphics that encourage continued collaboration from multiple intersecting fields.

Co-creation environment with cloud virtual reality and real-time artificial intelligence toward the design of molecular robots

This paper describes the design philosophy for our cloud-based virtual reality (VR) co-creation environment (CCE) for molecular modeling. Using interactive VR simulation can provide enhanced perspectives in molecular modeling for intuitive live demonstration and experimentation in the CCE. Then the use of the CCE can enhance knowledge creation by bringing people together to share and create ideas or knowledge that may not emerge otherwise. Our prototype CCE discussed here, which was developed to demonstrate our design philosophy, has already enabled multiple members to log in and touch virtual molecules running on a cloud server with no noticeable network latency via real-time artificial intelligence techniques. The CCE plays an essential role in the rational design of molecular robot parts, which consist of bio-molecules such as DNA and protein molecules.

Design - a new way to look at old molecules

We discuss how design enriches molecular science, particularly structural biology and bioinformatics. We present two use cases, one in academic practice and the other to design for outreach. The first case targets the representation of ion channels and their dynamic properties. In the second, we document a transition process from a research environment to general-purpose designs. Several testimonials from practitioners are given. By describing the design process of abstracted shapes, exploded views of molecular structures, motion-averaged slices, 360-degree panoramic projections, and experiments with lit sphere shading, we document how designers help make scientific data accessible without betraying its meaning, and how a creative mind adds value over purely data-driven visualizations. A similar conclusion was drawn for public outreach, as we found that comic-book-style drawings are better suited for communicating science to a broad audience.

Considering best practices in color palettes for molecular visualizations

Biomedical illustration and visualization techniques provide a window into complex molecular worlds that are difficult to capture through experimental means alone. Biomedical illustrators frequently employ color to help tell a molecular story, e.g., to identify key molecules in a signaling pathway. Currently, color use for molecules is largely arbitrary and often chosen based on the client, cultural factors, or personal taste. The study of molecular dynamics is relatively young, and some stakeholders argue that color use guidelines would throttle the growth of the field. Instead, content authors have ample creative freedom to choose an aesthetic that, e.g., supports the story they want to tell. However, such creative freedom comes at a price. The color design process is challenging, particularly for those without a background in color theory. The result is a semantically inconsistent color space that reduces the interpretability and effectiveness of molecular visualizations as a whole. Our contribution in this paper is threefold. We first discuss some of the factors that contribute to this array of color palettes. Second, we provide a brief sampling of color palettes used in both industry and research sectors. Lastly, we suggest considerations for developing best practices around color palettes applied to molecular visualization.

Strategies for the Production of Molecular Animations

Molecular animations play an increasing role in scientific visualisation and science communication. They engage viewers through non-fictional, documentary type storytelling and aim at advancing the audience. Every scene of a molecular animation is to be designed to secure clarity. To achieve this, knowledge on design principles from various design fields is essential. The relevant principles help to draw attention, guide the eye, establish relationships, convey dynamics and/or trigger a reaction. The tools of general graphic design are used to compose a signature frame, those of cinematic storytelling and user interface design to choreograph the relative movement of characters and cameras. Clarity in a scientific visualisation is reached by simplification and abstraction where the choice of the adequate representation is of great importance. A large set of illustration styles is available to chose the appropriate detail level but they are constrained by the availability of experimental data. For a high-quality molecular animation, data from different sources can be integrated, even filling the structural gaps to show a complete picture of the native biological situation. For maintaining scientific authenticity it is good practice to mark use of artistic licence which ensures transparency and accountability. The design of motion requires knowledge from molecule kinetics and kinematics. With biological macromolecules, four types of motion are most relevant: thermal motion, small and large conformational changes and Brownian motion. The principles of dynamic realism should be respected as well as the circumstances given in the crowded cellular environment. Ultimately, consistent complexity is proposed as overarching principle for the production of molecular animations and should be achieved between communication objective and abstraction/simplification, audience expertise and scientific complexity, experiment and representation, characters and environment as well as structure and motion representation.

An Automated Approach to Reasoning About Task-Oriented Insights in Responsive Visualization

Authors often transform a large screen visualization for smaller displays through rescaling, aggregation and other techniques when creating visualizations for both desktop and mobile devices (i.e., responsive visualization). However, transformations can alter relationships or patterns implied by the large screen view, requiring authors to reason carefully about what information to preserve while adjusting their design for the smaller display. We propose an automated approach to approximating the loss of support for task-oriented visualization insights (identification, comparison, and trend) in responsive transformation of a source visualization. We operationalize identification, comparison, and trend loss as objective functions calculated by comparing properties of the rendered source visualization to each realized target (small screen) visualization. To evaluate the utility of our approach, we train machine learning models on human ranked small screen alternative visualizations across a set of source visualizations. We find that our approach achieves an accuracy of 84% (random forest model) in ranking visualizations. We demonstrate this approach in a prototype responsive visualization recommender that enumerates responsive transformations using Answer Set Programming and evaluates the preservation of task-oriented insights using our loss measures. We discuss implications of our approach for the development of automated and semi-automated responsive visualization recommendation.

Structure of cell-cell adhesion mediated by the Down syndrome cell adhesion molecule

The Down syndrome cell adhesion molecule (DSCAM) belongs to the immunoglobulin superfamily (IgSF) and plays important roles in neural development. It has a large ectodomain, including 10 Ig-like domains and 6 fibronectin III (FnIII) domains. Previous data have shown that DSCAM can mediate cell adhesion by forming homophilic dimers between cells and contributes to self-avoidance of neurites or neuronal tiling, which is important for neural network formation. However, the organization and assembly of DSCAM at cell adhesion interfaces has not been fully understood. Here we combine electron microscopy and other biophysical methods to characterize the structure of the DSCAM-mediated cell adhesion and generate three-dimensional views of the adhesion interfaces of DSCAM by electron tomography. The results show that mouse DSCAM forms a regular pattern at the adhesion interfaces. The Ig-like domains contribute to both trans homophilic interactions and cis assembly of the pattern, and the FnIII domains are crucial for the cis pattern formation as well as the interaction with the cell membrane. By contrast, no obvious assembly pattern is observed at the adhesion interfaces mediated by mouse DSCAML1 or Drosophila DSCAMs, suggesting the different structural roles and mechanisms of DSCAMs in mediating cell adhesion and neural network formation.

Using sound to understand protein sequence data: new sonification algorithms for protein sequences and multiple sequence alignments

BACKGROUND

The use of sound to represent sequence data-sonification-has great potential as an alternative and complement to visual representation, exploiting features of human psychoacoustic intuitions to convey nuance more effectively. We have created five parameter-mapping sonification algorithms that aim to improve knowledge discovery from protein sequences and small protein multiple sequence alignments. For two of these algorithms, we investigated their effectiveness at conveying information. To do this we focussed on subjective assessments of user experience. This entailed a focus group session and survey research by questionnaire of individuals engaged in bioinformatics research.

RESULTS

For single protein sequences, the success of our sonifications for conveying features was supported by both the survey and focus group findings. For protein multiple sequence alignments, there was limited evidence that the sonifications successfully conveyed information. Additional work is required to identify effective algorithms to render multiple sequence alignment sonification useful to researchers. Feedback from both our survey and focus groups suggests future directions for sonification of multiple alignments: animated visualisation indicating the column in the multiple alignment as the sonification progresses, user control of sequence navigation, and customisation of the sound parameters.

CONCLUSIONS

Sonification approaches undertaken in this work have shown some success in conveying information from protein sequence data. Feedback points out future directions to build on the sonification approaches outlined in this paper. The effectiveness assessment process implemented in this work proved useful, giving detailed feedback and key approaches for improvement based on end-user input. The uptake of similar user experience focussed effectiveness assessments could also help with other areas of bioinformatics, for example in visualisation.

Production Processes for Creating Educational Videos

Asynchronous video-based educational resources allow for increased course material engagement. In today's climate, educators are encouraged to create videos for online instruction but are typically given limited production guidance. Few formal resources exist to guide educators for high-quality video production in a non-studio setting. This article is a how-to guide for producing videos using widely available primary resources through three steps: preproduction, production, and postproduction. During preproduction, educators consider style and project scope, including the "what, how, and why" of the content. For production, we have provided information on the set, light, sounds, and video equipment needed for optimizing video production in a non-studio setting. Finally, during postproduction, the educator considers how to combine and edit the video as well as organize content. Overall, this article is an approachable guide to help educators begin their low-budget video-production journeys.

Visualizing protein structures - tools and trends

Molecular visualization is fundamental in the current scientific literature, textbooks and dissemination materials. It provides an essential support for presenting results, reasoning on and formulating hypotheses related to molecular structure. Tools for visual exploration of structural data have become easily accessible on a broad variety of platforms thanks to advanced software tools that render a great service to the scientific community. These tools are often developed across disciplines bridging computer science, biology and chemistry. This mini-review was written as a short and compact overview for scientists who need to visualize protein structures and want to make an informed decision which tool they should use. Here, we first describe a few 'Swiss Army knives' geared towards protein visualization for everyday use with an existing large user base, then focus on more specialized tools for peculiar needs that are not yet as broadly known. Our selection is by no means exhaustive, but reflects a diverse snapshot of scenarios that we consider informative for the reader. We end with an account of future trends and perspectives.

Seeing the PDB

Ever since the first structures of proteins were determined in the 1960s, structural biologists have required methods to visualize biomolecular structures, both as an essential tool for their research and also to promote 3D comprehension of structural results by a wide audience of researchers, students, and the general public. In this review to celebrate the 50th anniversary of the Protein Data Bank, we present our own experiences in developing and applying methods of visualization and analysis to the ever-expanding archive of protein and nucleic acid structures in the worldwide Protein Data Bank. Across that timespan, Jane and David Richardson have concentrated on the organization inside and between the macromolecules, with ribbons to show the overall backbone "fold" and contact dots to show how the all-atom details fit together locally. David Goodsell has explored surface-based representations to present and explore biological subjects that range from molecules to cells. This review concludes with some ideas about the current challenges being addressed by the field of biomolecular visualization.

Elfin UI: A Graphical Interface for Protein Design With Modular Building Blocks

Molecular models have enabled understanding of biological structures and functions and allowed design of novel macro-molecules. Graphical user interfaces (GUIs) in molecular modeling are generally focused on atomic representations, but, especially for proteins, do not usually address designs of complex and large architectures, from nanometers to microns. Therefore, we have developed Elfin UI as a Blender add-on for the interactive design of large protein architectures with custom shapes. Elfin UI relies on compatible building blocks to design single- and multiple-chain protein structures. The software can be used: (1) as an interactive environment to explore building blocks combinations; and (2) as a computer aided design (CAD) tool to define target shapes that guide automated design. Elfin UI allows users to rapidly build new protein shapes, without the need to focus on amino acid sequence, and aims to make design of proteins and protein-based materials intuitive and accessible to researchers and members of the general public with limited expertise in protein engineering.

BlendMol: advanced macromolecular visualization in Blender

Summary

Programs such as VMD and PyMOL are excellent tools for analyzing macromolecular structures, but they do not implement many of the advanced rendering techniques common in the film and video-game industries. In contrast, the open-source program Blender is a general-purpose tool for industry-standard rendering/visualization, but its user interface is poorly suited for rigorous scientific analysis. We present BlendMol, a Blender plugin that imports VMD or PyMOL scenes into Blender. BlendMol-generated images are well suited for use in manuscripts, outreach programs, websites and classes.

Availability and implementation

BlendMol is available free of charge from http://durrantlab.com/blendmol/. It is written in Python.

Supplementary information

Supplementary data are available at Bioinformatics online.

Multi-Scale Procedural Animations of Microtubule Dynamics Based on Measured Data

Biologists often use computer graphics to visualize structures, which due to physical limitations are not possible to image with a microscope. One example for such structures are microtubules, which are present in every eukaryotic cell. They are part of the cytoskeleton maintaining the shape of the cell and playing a key role in the cell division. In this paper, we propose a scientifically-accurate multi-scale procedural model of microtubule dynamics as a novel application scenario for procedural animation, which can generate visualizations of their overall shape, molecular structure, as well as animations of the dynamic behaviour of their growth and disassembly. The model is spanning from tens of micrometers down to atomic resolution. All the aspects of the model are driven by scientific data. The advantage over a traditional, manual animation approach is that when the underlying data change, for instance due to new evidence, the model can be recreated immediately. The procedural animation concept is presented in its generic form, with several novel extensions, facilitating an easy translation to other domains with emergent multi-scale behavior.

Molecular Graphics: Bridging Structural Biologists and Computer Scientists

Visualization of molecular structures is one of the most common tasks carried out by structural biologists, typically using software, such as Chimera, COOT, PyMOL, or VMD. In this Perspective article, we outline how past developments in computer graphics and data visualization have expanded the understanding of biomolecular function, and we summarize recent advances that promise to further transform structural biology. We also highlight how progress in molecular graphics has been impeded by communication barriers between two communities: the computer scientists driving these advances, and the structural and computational biologists who stand to benefit. By pointing to canonical papers and explaining technical progress underlying new graphical developments in simple terms, we aim to improve communication between these communities; this, in turn, would help shape future developments in molecular graphics.

CellPAINT: Interactive Illustration of Dynamic Mesoscale Cellular Environments

CellPAINT allows nonexpert users to create interactive mesoscale illustrations that integrate a variety of biological data. Like popular digital painting software, scenes are created using a palette of molecular "brushes." The current release allows creation of animated scenes with an HIV virion, blood plasma, and a simplified T-cell.

Structural biology meets data science: does anything change?

Data science has emerged from the proliferation of digital data, coupled with advances in algorithms, software and hardware (e.g., GPU computing). Innovations in structural biology have been driven by similar factors, spurring us to ask: can these two fields impact one another in deep and hitherto unforeseen ways? We posit that the answer is yes. New biological knowledge lies in the relationships between sequence, structure, function and disease, all of which play out on the stage of evolution, and data science enables us to elucidate these relationships at scale. Here, we consider the above question from the five key pillars of data science: acquisition, engineering, analytics, visualization and policy, with an emphasis on machine learning as the premier analytics approach.

Visualization of Biomedical Data

The rapid increase in volume and complexity of biomedical data requires changes in research, communication, and clinical practices. This includes learning how to effectively integrate automated analysis with high–data density visualizations that clearly express complex phenomena. In this review, we summarize key principles and resources from data visualization research that help address this difficult challenge. We then survey how visualization is being used in a selection of emerging biomedical research areas, including three-dimensional genomics, single-cell RNA sequencing (RNA-seq), the protein structure universe, phosphoproteomics, augmented reality–assisted surgery, and metagenomics. While specific research areas need highly tailored visualizations, there are common challenges that can be addressed with general methods and strategies. Also common, however, are poor visualization practices. We outline ongoing initiatives aimed at improving visualization practices in biomedical research via better tools, peer-to-peer learning, and interdisciplinary collaboration with computer scientists, science communicators, and graphic designers. These changes are revolutionizing how we see and think about our data.

Molecular Illustration in Research and Education: Past, Present, and Future

Two-dimensional illustration is used extensively to study and disseminate the results of structural molecular biology. Molecular graphics methods have been and continue to be developed to address the growing needs of the structural biology community, and there are currently many effective, turn-key methods for displaying and exploring molecular structure. Building on decades of experience in design, best-practice resources are available to guide creation of illustrations that are effective for research and education communities.

Instant Construction and Visualization of Crowded Biological Environments

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-interactive environment. Our solution unites the modeling and visualization aspect, enabling interactive construction of atomic resolution mesoscale models of large portions of a cell. We present a novel set of GPU algorithms that build the basis for the rapid construction of complex biological structures. These structures consist of multiple membrane-enclosed compartments including both soluble molecules and fibrous structures. The compartments are defined using volume voxelization of triangulated meshes. For membranes, we present an extension of the Wang Tile concept that populates the bilayer with individual lipids. Soluble molecules are populated within compartments distributed according to a Halton sequence. Fibrous structures, such as RNA or actin filaments, are created by self-avoiding random walks. Resulting overlaps of molecules are resolved by a forced-based system. Our approach opens new possibilities to the world of interactive construction of cellular compartments. We demonstrate its effectiveness by showcasing scenes of different scale and complexity that comprise blood plasma, mycoplasma, and HIV.

The Scientist as Illustrator

Proficiency in art and illustration was once considered an essential skill for biologists, because text alone often could not suffice to describe observations of biological systems. With modern imaging technology, it is no longer necessary to illustrate what we can see by eye. However, in molecular and cellular biology, our understanding of biological processes is dependent on our ability to synthesize diverse data to generate a hypothesis. Creating visual models of these hypotheses is important for generating new ideas and for communicating to our peers and to the public. Here, I discuss the benefits of creating visual models in molecular and cellular biology and consider steps to enable researchers to become more effective visual communicators.

Creating Stop-Motion Animations to Learn Molecular Biology Dynamics

Classes in molecular biology have historically used static diagrams to capture how molecular processes occur in space and time. Here we describe using 3D claymation as an alternative. Students choose a molecular process, plan how to represent it with physical objects, and produce a stop motion video that then is shared with other students over the internet. This process can be easily implemented in undergraduate biology classes at all levels, and requires very little resources. The exercise offers the students a multisensory learning experience and the opportunity to contribute to open education resources.

Quantifying Modes of 3D Cell Migration

Although it is widely appreciated that cells migrate in a variety of diverse environments in vivo, we are only now beginning to use experimental workflows that yield images with sufficient spatiotemporal resolution to study the molecular processes governing cell migration in 3D environments. Since cell migration is a dynamic process, it is usually studied via microscopy, but 3D movies of 3D processes are difficult to interpret by visual inspection. In this review, we discuss the technologies required to study the diversity of 3D cell migration modes with a focus on the visualization and computational analysis tools needed to study cell migration quantitatively at a level comparable to the analyses performed today on cells crawling on flat substrates.

Multidomain Assembler (MDA) Generates Models of Large Multidomain Proteins

Homology modeling predicts protein structures using known structures of related proteins as templates. We developed MULTIDOMAIN ASSEMBLER (MDA) to address the special problems that arise when modeling proteins with large numbers of domains, such as fibronectin with 30 domains, as well as cases with hundreds of templates. These problems include how to spatially arrange nonoverlapping template structures, and how to get the best template coverage when some sequence regions have hundreds of available structures while other regions have a few distant homologs. MDA automates the tasks of template searching, visualization, and selection followed by multidomain model generation, and is part of the widely used molecular graphics package UCSF CHIMERA (University of California, San Francisco). We demonstrate applications and discuss MDA's benefits and limitations.

SOCR data dashboard: an integrated big data archive mashing medicare, labor, census and econometric information

INTRODUCTION

Intuitive formulation of informative and computationally-efficient queries on big and complex datasets present a number of challenges. As data collection is increasingly streamlined and ubiquitous, data exploration, discovery and analytics get considerably harder. Exploratory querying of heterogeneous and multi-source information is both difficult and necessary to advance our knowledge about the world around us.

RESEARCH DESIGN

We developed a mechanism to integrate dispersed multi-source data and service the mashed information via human and machine interfaces in a secure, scalable manner. This process facilitates the exploration of subtle associations between variables, population strata, or clusters of data elements, which may be opaque to standard independent inspection of the individual sources. This a new platform includes a device agnostic tool (Dashboard webapp, http://socr.umich.edu/HTML5/Dashboard/) for graphical querying, navigating and exploring the multivariate associations in complex heterogeneous datasets.

RESULTS

The paper illustrates this core functionality and serviceoriented infrastructure using healthcare data (e.g., US data from the 2010 Census, Demographic and Economic surveys, Bureau of Labor Statistics, and Center for Medicare Services) as well as Parkinson's Disease neuroimaging data. Both the back-end data archive and the front-end dashboard interfaces are continuously expanded to include additional data elements and new ways to customize the human and machine interactions.

CONCLUSIONS

A client-side data import utility allows for easy and intuitive integration of user-supplied datasets. This completely open-science framework may be used for exploratory analytics, confirmatory analyses, meta-analyses, and education and training purposes in a wide variety of fields.