Visualization of macromolecular structures

Modulation of a Loop Region in the Substrate Binding Pocket Affects the Degree of Polymerization of Bacillus subtilis Chitosanase Products

The hydrolytic products of chitosanase from Streptomyces avermitilis (SaCsn46A) were found to be aminoglucose and chitobiose, whereas those of chitosanase from Bacillus subtilis (BsCsn46A) were chitobiose and chitotriose. Therefore, the sequence alignment between SaCsn46A and BsCsn46A was conducted, revealing that the structure of BsCsn46A possesses an extra loop region (194N-200T) at the substrate binding pocket. To clarify the impact of this loop on hydrolytic properties, three mutants, SC, TJN, and TJA, were constructed. Eventually, the experimental results indicated that SC changed the ratio of chitobiose to chitotriose hydrolyzed by chitosanase from 1:1 into 2:3, while TJA resulted in a ratio of 15:7. This experiment combined molecular research to unveil a crucial loop within the substrate binding pocket of chitosanase. It also provides an effective strategy for mutagenesis and a foundation for altering hydrolysate composition and further applications in engineering chitosanase.

PlayMolecule Viewer: A Toolkit for the Visualization of Molecules and Other Data

PlayMolecule Viewer is a web-based data visualization toolkit designed to streamline the exploration of data resulting from structural bioinformatics or computer-aided drug design efforts. By harnessing state-of-the-art web technologies such as WebAssembly, PlayMolecule Viewer integrates powerful Python libraries directly within the browser environment, which enhances its capabilities to manage multiple types of molecular data. With its intuitive interface, it allows users to easily upload, visualize, select, and manipulate molecular structures and associated data. The toolkit supports a wide range of common structural file formats and offers a variety of molecular representations to cater to different visualization needs. PlayMolecule Viewer is freely accessible at open.playmolecule.org, ensuring accessibility and availability to the scientific community and beyond.

Enhancing the thermostability and catalytic activity of Bacillus subtilis chitosanase by saturation mutagenesis of Lys242

Catalysis activity and thermostability are some of the fundamental characteristic of enzymes, which are of great significance to their industrial applications. Bacillus subtilis chitosanase BsCsn46A is a kind of enzyme with good catalytic activity and stability, which can hydrolyze chitosan to produce chitobiose and chitotriose. In order to further improve the catalytic activity and stability of BsCsn46A, saturation mutagenesis of the C-terminal K242 of BsCsn46A was performed. The results showed that the six mutants (K242A, K242D, K242E, K242F, K242P, and K242T) showed increased catalytic activity on chitosan. The catalytic activity of K242P increased from 12971 ± 597 U mg-1 of wild type to 17820 ± 344 U mg-1 , and the thermostability of K242P increased by 2.27%. In order to elucidate the reason for the change of enzymatic properties, hydrogen network, molecular docking, and molecular dynamics simulation were carried out. The hydrogen network results showed that all the mutants lose their interaction with Asp6 at 242 site, thereby increasing the flexibility of Glu19 at the junction sites of α1 and loop1. Molecular dynamics results showed that the RMSD of K242P was lower at both 313 and 323 K than that of other mutants, which supported that K242P had better thermostability. The catalytic activity of mutant K242P reached 17820.27 U mg-1 , the highest level reported so far, which could be a robust candidate for the industrial application of chitooligosaccharide (COS) production.

PDBImages: a command-line tool for automated macromolecular structure visualization

SUMMARY

PDBImages is an innovative, open-source Node.js package that harnesses the power of the popular macromolecule structure visualization software Mol*. Designed for use by the scientific community, PDBImages provides a means to generate high-quality images for PDB and AlphaFold DB models. Its unique ability to render and save images directly to files in a browserless mode sets it apart, offering users a streamlined, automated process for macromolecular structure visualization. Here, we detail the implementation of PDBImages, enumerating its diverse image types, and elaborating on its user-friendly setup. This powerful tool opens a new gateway for researchers to visualize, analyse, and share their work, fostering a deeper understanding of bioinformatics.

AVAILABILITY AND IMPLEMENTATION

PDBImages is available as an npm package from https://www.npmjs.com/package/pdb-images. The source code is available from https://github.com/PDBeurope/pdb-images.

A tRNAModification-based strategy for Identifying amiNo acid Overproducers (AMINO)

Amino acids have a multi-billion-dollar market with rising demand, prompting the development of high-performance microbial factories. However, a general screening strategy applicable to all proteinogenic and non-proteinogenic amino acids is still lacking. Modification of the critical structure of tRNA could decrease the aminoacylation level of tRNA catalyzed by aminoacyl-tRNA synthetases. Involved in a two-substrate sequential reaction, amino acids with increased concentration could elevate the reduced aminoacylation rate caused by specific tRNA modification. Here, we developed a selection system for overproducers of specific amino acids using corresponding engineered tRNAs and marker genes. As a proof-of-concept, overproducers of five amino acids such as L-tryptophan were screened out by growth-based and/or fluorescence-activated cell sorting (FACS)-based screening from random mutation libraries of Escherichia coli and Corynebacterium glutamicum, respectively. This study provided a universal strategy that could be applied to screen overproducers of proteinogenic and non-proteinogenic amino acids in amber-stop-codon-recoded or non-recoded hosts.

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.

Thr22 plays an important role in the efficient catalytic process of Bacillus subtilis chitosanase BsCsn46A

Threonine 22 (Thr22) located in catalytic center near the catalytic amino acid Glu19 was non-conserved in Bacillus species chitosanase. In order to study the function of Thr22, saturation mutagenesis was carried out towards P121N, a mutant previously constructed in our laboratory. Compared with P121N, which was designated as the wild type (WT) in this research, the specific enzyme activity of all mutants was decreased, and that of the T22P mutant was decreased by 91.6 %. Among these mutants, the optimum temperature decreased from 55 °C to 50 °C for 10 mutants and 45 °C for 4 mutants, respectively. The optimum temperature of mutant T22P was 40 °C. In order to analyze the reasons for the changes in enzymatic properties of the mutants, molecular docking analysis of WT and its mutants with substrate were performed. The hydrogen bond analysis around position 22 also conducted. The substitution of Thr22 was found to significantly affect the enzyme-substrate complex interaction. In addition, the hydrogen network near position 22 has undergone obvious changes. These changes may be the main reasons for the changes in enzymatic properties of the mutants. Altogether, this study is valuable for the future research on Bacillus chitosanase.

Enhancing Enzyme Activity and Thermostability of Bacillus amyloliquefaciens Chitosanase BaCsn46A Through Saturation Mutagenesis at Ser196

Chitosanase plays an important role in chitooligosaccharides (COS) production. We found that the chitosanase (BaCsn46A) of Bacillus amyloliquefacien was a good candidate for chitosan hydrolysis of COS. In order to further improve the enzyme properties of BaCsn46A, the S196 located near the active center was found to be a critical site impacts on enzyme properties by sequence alignment analysis. Herein, saturation mutation was carried out to study role of 196 site on BaCsn46A catalytic function. Compared with WT, the specific enzyme activity of S196A increased by 118.79%, and the thermostability of S196A was much higher than WT. In addition, we found that the enzyme activity of S196P was 2.41% of that of WT, indicating that the type of amino acid in 196 site could significant affect the catalytic activity and thermostability of BaCsn46A. After molecular docking analysis we found that the increase in hydrogen bonds and decrease in unfavorable bonds interacting with the substrate were the main reason for the change of enzyme properties which is valuable for future studies on Bacillus species chitosanase.

A brief history of visualizing membrane systems in molecular dynamics simulations

Understanding lipid dynamics and function, from the level of single, isolated molecules to large assemblies, is more than ever an intensive area of research. The interactions of lipids with other molecules, particularly membrane proteins, are now extensively studied. With advances in the development of force fields for molecular dynamics simulations (MD) and increases in computational resources, the creation of realistic and complex membrane systems is now common. In this perspective, we will review four decades of the history of molecular dynamics simulations applied to membranes and lipids through the prism of molecular graphics.

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.

Network pharmacology of iridoid glycosides from Eucommia ulmoides Oliver against osteoporosis

Eucommia ulmoides Oliver is one of the commonly used traditional Chinese medicines for the treatment of osteoporosis, and iridoid glycosides are considered to be its active ingredients against osteoporosis. This study aims to clarify the chemical components and molecular mechanism of iridoid glycosides of Eucommia ulmoides Oliver in the treatment of osteoporosis by integrating network pharmacology and molecular simulations. The active iridoid glycosides and their potential targets were retrieved from text mining as well as Swiss Target Prediction, TargetNet database, and STITCH databases. At the same time, DisGeNET, GeneCards, and Therapeutic Target Database were used to search for the targets associated with osteoporosis. A protein–protein interaction network was built to analyze the interactions between targets. Then, DAVID bioinformatics resources and R 3.6.3 project were used to carry out Gene Ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis. Moreover, interactions between active compounds and potential targets were investigated through molecular docking, molecular dynamic simulation, and binding free energy analysis. The results showed that a total of 12 iridoid glycosides were identified as the active iridoid glycosides of Eucommia ulmoides Oliver in the treatment of osteoporosis. Among them, aucubin, reptoside, geniposide and ajugoside were the core compounds. The enrichment analysis suggested iridoid glycosides of Eucommia ulmoides Oliver prevented osteoporosis mainly through PI3K-Akt signaling pathway, MAPK signaling pathway and Estrogen signaling pathway. Molecular docking results indicated that the 12 iridoid glycosides had good binding ability with 25 hub target proteins, which played a critical role in the treatment of osteoporosis. Molecular dynamic and molecular mechanics Poisson–Boltzmann surface area results revealed these compounds showed stable binding to the active sites of the target proteins during the simulations. In conclusion, our research demonstrated that iridoid glycosides of Eucommia ulmoides Oliver in the treatment of osteoporosis involved a multi-component, multi-target and multi-pathway mechanism, which provided new suggestions and theoretical support for treating osteoporosis.

Vectorial channeling as a mechanism for translational control by functional prions and condensates

Translation of messenger RNA (mRNA) is regulated through a diverse set of RNA-binding proteins. A significant fraction of RNA-binding proteins contains prion-like domains which form functional prions. This raises the question of how prions can play a role in translational control. Local control of translation in dendritic spines by prions has been invoked in the mechanism of synaptic plasticity and memory. We show how channeling through diffusion and processive translation cooperate in highly ordered mRNA/prion aggregates as well as in less ordered mRNA/protein condensates depending on their substructure. We show that the direction of translational control, whether it is repressive or activating, depends on the polarity of the mRNA distribution in mRNA/prion assemblies which determines whether vectorial channeling can enhance recycling of ribosomes. Our model also addresses the effect of changes of substrate concentration in assemblies that have been suggested previously to explain translational control by assemblies through the introduction of a potential of mean force biasing diffusion of ribosomes inside the assemblies. The results from the model are compared with the experimental data on translational control by two functional RNA-binding prions, CPEB involved in memory and Rim4 involved in gametogenesis.

Improvement of the Catalytic Activity of Chitosanase BsCsn46A from Bacillus subtilis by Site-Saturation Mutagenesis of Proline121

BsCsn46A, a GH46 family chitosanase from Bacillus subtilis, has great potential for industrial chitooligosaccharide production due to its high activity and stability. In this study, a special amino acid Pro121 was identified not fit in the helix structure, which was located in the opposite side of the active center in BsCsn46A, by the PoPMuSiC algorithm. Then, saturation mutagenesis was performed to explore the role of the site amino acid 121. Compared with the wild type, the specific activity of P121N, P121C, and P121V was increased by 1.69-, 1.97-, and 2.15-fold, respectively. In particular, the specific activity of P121N was increased without loss of thermostability, indicating that replacing the structural stiffness of proline in the helical structure could significantly improve the chitosanase activity. The K_m values of P121N, P121C, and P121V decreased significantly, indicating that the affinity between the enzyme-substrate complex was enhanced. Through molecular docking, it was found that the increase of hydrogen bonds and van der Waals force between the enzyme-substrate complex and the removal of unfavorable bonds might be the main reason for the change of enzyme properties. In addition, the optimal temperature of the three mutants changed from 60 to 55 °C. These results indicate that the site 121 plays a critical role in the catalytic activity and enzymatic properties of chitosanase. To our knowledge, the results provide novel data on chitosanase activity and identify an excellent candidate of industrial chitosanase.

Protein-protein interactions at a glance: Protocols for the visualization of biomolecular interactions

Protein-protein interactions (PPIs) play a key role in many biological processes and are intriguing targets for drug discovery campaigns. Advancements in experimental and computational techniques are leading to a growth of data accessibility, and, with it, an increased need for the analysis of PPIs. In this respect, visualization tools are essential instruments to represent and analyze biomolecular interactions. In this chapter, we reviewed some of the available tools, highlighting their features, and describing their functions with practical information on their usage.

VRmol: an integrative web-based virtual reality system to explore macromolecular structure

SUMMARY

Structural visualization and analysis are fundamental to explore macromolecular functions. Here, we present a novel integrative web-based virtual reality (VR) system-VRmol, to visualize and study molecular structures in an immersive virtual environment. Importantly, it is integrated with multiple online databases and is able to couple structure studies with associated genomic variations and drug information in a visual interface by cloud-based drug docking. VRmol thus can serve as an integrative platform to aid structure-based translational research and drug design.

AVAILABILITY AND IMPLEMENTATION

VRmol is freely available (https://VRmol.net), with detailed manual and tutorial (https://VRmol.net/docs). The code of VRmol is available as open source under the MIT license at http://github.com/kuixu/VRmol.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

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.

UCSF ChimeraX: Structure visualization for researchers, educators, and developers

UCSF ChimeraX is the next-generation interactive visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. ChimeraX brings (a) significant performance and graphics enhancements; (b) new implementations of Chimera's most highly used tools, many with further improvements; (c) several entirely new analysis features; (d) support for new areas such as virtual reality, light-sheet microscopy, and medical imaging data; (e) major ease-of-use advances, including toolbars with icons to perform actions with a single click, basic "undo" capabilities, and more logical and consistent commands; and (f) an app store for researchers to contribute new tools. ChimeraX includes full user documentation and is free for noncommercial use, with downloads available for Windows, Linux, and macOS from https://www.rbvi.ucsf.edu/chimerax.

Art and Science of the Cellular Mesoscale

Experimental information from microscopy, structural biology, and bioinformatics may be integrated to build structural models of entire cells with molecular detail. This integrative modeling is challenging in several ways: the intrinsic complexity of biology results in models with many closely packed and heterogeneous components; the wealth of available experimental data is scattered among multiple resources and must be gathered, reconciled, and curated; and computational infrastructure is only now gaining the capability of modeling and visualizing systems of this complexity. We present recent efforts to address these challenges, both with artistic approaches to depicting the cellular mesoscale, and development and application of methods to build quantitative models.

Visualization and Analysis of Protein Structures with LiteMol Suite

LiteMol suite is an innovative solution that enables near-instant delivery of model and experimental biomacromolecular structural data, providing users with an interactive and responsive experience in all modern web browsers and mobile devices. LiteMol suite is a combination of data delivery services (CoordinateServer and DensityServer), compression format (BinaryCIF), and a molecular viewer (LiteMol Viewer). The LiteMol suite is integrated into Protein Data Bank in Europe (PDBe) and other life science web applications (e.g., UniProt, Ensemble, SIB, and CNRS services), it is freely available at https://litemol.org , and its source code is available via GitHub. LiteMol suite provides advanced functionality (annotations and their visualization, powerful selection features), and this chapter will describe their use for visual inspection of protein structures.

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.

Illustrate: Software for Biomolecular Illustration

The small program Illustrate generates non-photorealistic images of biological molecules for use in dissemination, outreach, and education. The method has been used as part of the "Molecule of the Month," an ongoing educational column at the RCSB Protein Data Bank (http://rcsb.org). Insights from 20 years of application of the program are presented, and the program has been released both as open-source Fortran at GitHub and through an interactive web-based interface.

Web3DMol: interactive protein structure visualization based on WebGL

A growing number of web-based databases and tools for protein research are being developed. There is now a widespread need for visualization tools to present the three-dimensional (3D) structure of proteins in web browsers. Here, we introduce our 3D modeling program—Web3DMol—a web application focusing on protein structure visualization in modern web browsers. Users submit a PDB identification code or select a PDB archive from their local disk, and Web3DMol will display and allow interactive manipulation of the 3D structure. Featured functions, such as sequence plot, fragment segmentation, measure tool and meta-information display, are offered for users to gain a better understanding of protein structure. Easy-to-use APIs are available for developers to reuse and extend Web3DMol. Web3DMol can be freely accessed at http://web3dmol.duapp.com/, and the source code is distributed under the MIT license.

Molecular Interaction-Based Exploration of the Broad Spectrum Efficacy of a Bacillus thuringiensis Insecticidal Chimeric Protein, Cry1AcF

Bacillus thuringiensis insecticidal proteins (Bt ICPs) are reliable and valuable options for pest management in crops. Protein engineering of Bt ICPs is a competitive alternative for resistance management in insects. The primary focus of the study was to reiterate the translational utility of a protein-engineered chimeric Cry toxin, Cry1AcF, for its broad spectrum insecticidal efficacy using molecular modeling and docking studies. In-depth bioinformatic analysis was undertaken for structure prediction of the Cry toxin as the ligand and aminopeptidase1 receptors (APN1) from Helicoverpa armigera (HaAPN1) and Spodoptera litura (SlAPN1) as receptors, followed by interaction studies using protein-protein docking tools. The study revealed feasible interactions between the toxin and the two receptors through H-bonding and hydrophobic interactions. Further, molecular dynamics simulations substantiated the stability of the interactions, proving the broad spectrum efficacy of Cry1AcF in controlling H. armigera and S. litura. These findings justify the utility of protein-engineered toxins in pest management.

Communicating Genome Architecture: Biovisualization of the Genome, from Data Analysis and Hypothesis Generation to Communication and Learning

Genome discoveries at the core of biology are made by visual description and exploration of the cell, from microscopic sketches and biochemical mapping to computational analysis and spatial modeling. We outline the experimental and visualization techniques that have been developed recently which capture the three-dimensional interactions regulating how genes are expressed. We detail the challenges faced in integration of the data to portray the components and organization and their dynamic landscape. The goal is more than a single data-driven representation as interactive visualization for de novo research is paramount to decipher insights on genome organization in space.

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.

Perspectives on Structural Molecular Biology Visualization: From Past to Present

Visualization has been a key technology in the progress of structural molecular biology for as long as the field has existed. This perspective describes the nature of the visualization process in structural studies, how it has evolved over the years, and its relationship to the changes in technology that have supported and driven it. It focuses on how technical advances have changed the way we look at and interact with molecular structure, and how structural biology has fostered and challenged that technology.

Navigating Among Known Structures in Protein Space

Present-day protein space is the result of 3.7 billion years of evolution, constrained by the underlying physicochemical qualities of the proteins. It is difficult to differentiate between evolutionary traces and effects of physicochemical constraints. Nonetheless, as a rule of thumb, instances of structural reuse, or focusing on structural similarity, are likely attributable to physicochemical constraints, whereas sequence reuse, or focusing on sequence similarity, may be more indicative of evolutionary relationships. Both types of relationships have been studied and can provide meaningful insights to protein biophysics and evolution, which in turn can lead to better algorithms for protein search, annotation, and maybe even design.In broad strokes, studies of protein space vary in the entities they represent, the similarity measure comparing these entities, and the representation used. The entities can be, for example, protein chains, domains, supra-domains, or smaller protein sub-parts denoted themes. The measures of similarity between the entities can be based on sequence, structure, function, or any combination of these. The representation can be global, encompassing the whole space, or local, focusing on a particular region surrounding protein(s) of interest. Global representations include lists of grouped proteins, protein networks, and maps. Networks are the abstraction that is derived most directly from the similarity data: each node is the protein entity (e.g., a domain), and edges connect similar domains. Selecting the entities, the similarity measure, and the abstraction are three intertwined decisions: the similarity measures allow us to identify the entities, and the selection of entities influences what is a meaningful similarity measure. Similarly, we seek entities that are related to each other in a way, for which a simple representation describes their relationships succinctly and accurately. This chapter will cover studies that rely on different entities, similarity measures, and a range of representations to better understand protein structure space. Scholars may use publicly available navigators offering a global representation, and in particular the hierarchical classifications SCOP, CATH, and ECOD, or a local representation, which encompass structural alignment algorithms. Alternatively, scholars can configure their own navigator using existing tools. To demonstrate this DIY (do it yourself) approach for navigating in protein space, we investigate substrate-binding proteins. By presenting sequence similarities among this large and diverse protein family as a network, we can infer that one member (pdb ID 4ntl; of yet unknown function) may bind methionine and suggest a putative binding mechanism.

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.

Semantics for an Integrative and Immersive Pipeline Combining Visualization and Analysis of Molecular Data

The advances made in recent years in the field of structural biology significantly increased the throughput and complexity of data that scientists have to deal with. Combining and analyzing such heterogeneous amounts of data became a crucial time consumer in the daily tasks of scientists. However, only few efforts have been made to offer scientists an alternative to the standard compartmentalized tools they use to explore their data and that involve a regular back and forth between them. We propose here an integrated pipeline especially designed for immersive environments, promoting direct interactions on semantically linked 2D and 3D heterogeneous data, displayed in a common working space. The creation of a semantic definition describing the content and the context of a molecular scene leads to the creation of an intelligent system where data are (1) combined through pre-existing or inferred links present in our hierarchical definition of the concepts, (2) enriched with suitable and adaptive analyses proposed to the user with respect to the current task and (3) interactively presented in a unique working environment to be explored.

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.

Making data matter: Voxel printing for the digital fabrication of data across scales and domains

We present a multimaterial voxel-printing method that enables the physical visualization of data sets commonly associated with scientific imaging. Leveraging voxel-based control of multimaterial three-dimensional (3D) printing, our method enables additive manufacturing of discontinuous data types such as point cloud data, curve and graph data, image-based data, and volumetric data. By converting data sets into dithered material deposition descriptions, through modifications to rasterization processes, we demonstrate that data sets frequently visualized on screen can be converted into physical, materially heterogeneous objects. Our approach alleviates the need to postprocess data sets to boundary representations, preventing alteration of data and loss of information in the produced physicalizations. Therefore, it bridges the gap between digital information representation and physical material composition. We evaluate the visual characteristics and features of our method, assess its relevance and applicability in the production of physical visualizations, and detail the conversion of data sets for multimaterial 3D printing. We conclude with exemplary 3D-printed data sets produced by our method pointing toward potential applications across scales, disciplines, and problem domains.

Developing novel methods to image and visualize 3D genomes

To investigate three-dimensional (3D) genome organization in prokaryotic and eukaryotic cells, three main strategies are employed, namely nuclear proximity ligation-based methods, imaging tools (such as fluorescence in situ hybridization (FISH) and its derivatives), and computational/visualization methods. Proximity ligation-based methods are based on digestion and re-ligation of physically proximal cross-linked chromatin fragments accompanied by massively parallel DNA sequencing to measure the relative spatial proximity between genomic loci. Imaging tools enable direct visualization and quantification of spatial distances between genomic loci, and advanced implementation of (super-resolution) microscopy helps to significantly improve the resolution of images. Computational methods are used to map global 3D genome structures at various scales driven by experimental data, and visualization methods are used to visualize genome 3D structures in virtual 3D space-based on algorithms. In this review, we focus on the introduction of novel imaging and visualization methods to study 3D genomes. First, we introduce the progress made recently in 3D genome imaging in both fixed cell and live cells based on long-probe labeling, short-probe labeling, RNA FISH, and the CRISPR system. As the fluorescence-capturing capability of a particular microscope is very important for the sensitivity of bioimaging experiments, we also introduce two novel super-resolution microscopy methods, SDOM and low-power super-resolution STED, which have potential for time-lapse super-resolution live-cell imaging of chromatin. Finally, we review some software tools developed recently to visualize proximity ligation-based data. The imaging and visualization methods are complementary to each other, and all three strategies are not mutually exclusive. These methods provide powerful tools to explore the mechanisms of gene regulation and transcription in cell nuclei.

Structural Class Classification of 3D Protein Structure Based on Multi-View 2D Images

Computing similarity or dissimilarity between protein structures is an important task in structural biology. A conventional method to compute protein structure dissimilarity requires structural alignment of the proteins. However, defining one best alignment is difficult, especially when the structures are very different. In this paper, we propose a new similarity measure for protein structure comparisons using a set of multi-view 2D images of 3D protein structures. In this approach, each protein structure is represented by a subspace from the image set. The similarity between two protein structures is then characterized by the canonical angles between the two subspaces. The primary advantage of our method is that precise alignment is not needed. We employed Grassmann Discriminant Analysis (GDA) as the subspace-based learning in the classification framework. We applied our method for the classification problem of seven SCOP structural classes of protein 3D structures. The proposed method outperformed the k-nearest neighbor method (k-NN) based on conventional alignment-based methods CE, FATCAT, and TM-align. Our method was also applied to the classification of SCOP folds of membrane proteins, where the proposed method could recognize the fold HEM-binding four-helical bundle (f.21) much better than TM-Align.

UCSF ChimeraX: Meeting modern challenges in visualization and analysis

UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax/ for Windows, Mac, and Linux.

The Science Behind G Protein-Coupled Receptors (GPCRs) and Their Accurate Visual Representation in Scientific Research

G Protein-Coupled Receptors (GPCRs) are transmembrane (TM) proteins that span the cell membrane seven times, and contain intracellular and extracellular domains, comprised of connecting loops, as well as terminal extension sequences. GPCRs bind ligands within their transmembrane and/or extracellular domains. Ligand binding elicits conformational changes that initiate downstream intracellular signaling events through arrestins and G proteins. GPCRs play central roles in many physiological processes, from sensory to neurological, cardiovascular, endocrine, and reproductive functions. This paper strives to provide an entry point to current GPCR science, and to identify visual approaches to communicate select aspects of GPCR structure and function with clarity and accuracy. The overall GPCR structure, primary sequence and the implications of sequence for membrane topology, ligand binding and helical rearrangements accompanying activation are considered and discussed in the context of visualization strategies, including two-dimensional topological diagrams, three-dimensional representations, and common errors that arise from these representations.

PyMOL mControl: Manipulating molecular visualization with mobile devices

Viewing and manipulating three-dimensional (3D) structures in molecular graphics software are essential tasks for researchers and students to understand the functions of molecules. Currently, the way to manipulate a 3D molecular object is mainly based on mouse-and-keyboard control that is usually difficult and tedious to learn. While gesture-based and touch-based interactions are increasingly popular in interactive software systems, their suitability in handling molecular graphics has not yet been sufficiently explored. Here, we designed the gesture-based and touch-based interaction methods to manipulate virtual objects in PyMOL utilizing the motion and touch sensors in a mobile device. Three fundamental viewing controls-zooming, translation and rotation-and frequently used functions were implemented. Results from a pilot user study reveal that task performances on viewing controls using a mobile device are slightly reduced as compared to mouse-and-keyboard method. However, it is considered to be more suitable for oral presentations and equally suitable for education scenarios such as school classes. Overall, PyMOL mControl provides an alternative way to manipulate objects in molecular graphic software with new user experiences. The software is freely available at http://cbbio.cis.umac.mo/mcontrol.html. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(1):76-83, 2017.

The RCSB protein data bank: integrative view of protein, gene and 3D structural information

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, http://rcsb.org), the US data center for the global PDB archive, makes PDB data freely available to all users, from structural biologists to computational biologists and beyond. New tools and resources have been added to the RCSB PDB web portal in support of a ‘Structural View of Biology.’ Recent developments have improved the User experience, including the high-speed NGL Viewer that provides 3D molecular visualization in any web browser, improved support for data file download and enhanced organization of website pages for query, reporting and individual structure exploration. Structure validation information is now visible for all archival entries. PDB data have been integrated with external biological resources, including chromosomal position within the human genome; protein modifications; and metabolic pathways. PDB-101 educational materials have been reorganized into a searchable website and expanded to include new features such as the Geis Digital Archive.

Visualizing ensembles in structural biology

Displaying a single representative conformation of a biopolymer rather than an ensemble of states mistakenly conveys a static nature rather than the actual dynamic personality of biopolymers. However, there are few apparent options due to the fixed nature of print media. Here we suggest a standardized methodology for visually indicating the distribution width, standard deviation and uncertainty of ensembles of states with little loss of the visual simplicity of displaying a single representative conformation. Of particular note is that the visualization method employed clearly distinguishes between isotropic and anisotropic motion of polymer subunits. We also apply this method to ligand binding, suggesting a way to indicate the expected error in many high throughput docking programs when visualizing the structural spread of the output. We provide several examples in the context of nucleic acids and proteins with particular insights gained via this method. Such examples include investigating a therapeutic polymer of FdUMP (5-fluoro-2-deoxyuridine-5-O-monophosphate) - a topoisomerase-1 (Top1), apoptosis-inducing poison - and nucleotide-binding proteins responsible for ATP hydrolysis from Bacillus subtilis. We also discuss how these methods can be extended to any macromolecular data set with an underlying distribution, including experimental data such as NMR structures.

A Review on the Bioinformatics Tools for Neuroimaging

Neuroimaging is a new technique used to create images of the structure and function of the nervous system in the human brain. Currently, it is crucial in scientific fields. Neuroimaging data are becoming of more interest among the circle of neuroimaging experts. Therefore, it is necessary to develop a large amount of neuroimaging tools. This paper gives an overview of the tools that have been used to image the structure and function of the nervous system. This information can help developers, experts, and users gain insight and a better understanding of the neuroimaging tools available, enabling better decision making in choosing tools of particular research interest. Sources, links, and descriptions of the application of each tool are provided in this paper as well. Lastly, this paper presents the language implemented, system requirements, strengths, and weaknesses of the tools that have been widely used to image the structure and function of the nervous system.

Pediatric Pathology In The Year 2050

The study of pathology in fetuses, infants, and children had its beginnings in the mid-19th century. Now, 165 years later, hundreds of pediatric pathologists are in up-to-date practices throughout the world. They, and all medical practitioners, are just beginning to delve into the nanotechnical wave. Nanotechnology refers to the structure and activity of minute particles, molecules, compounds, and atoms. By 2050, as nanotechnical studies develop further, new diseases and variations of old diseases will be discovered. Aggregation of medical data from billions of people, a process known as crowd sourcing, will be digitally interconnected to the new findings with computers. Pediatric pathologists will contribute to this expanding science with new laboratory instruments, including ultramodern microscopes known as Omniscopes. Robots will be programmed to perform autopsies and process surgical specimens. Analyzers in chemistry, microbiology, hematology, and genetics will, in 2050, produce dozens or even hundreds of results within minutes. These advances will lead to better treatments and overall better health for everyone.

NGL Viewer: a web application for molecular visualization

The NGL Viewer (http://proteinformatics.charite.de/ngl) is a web application for the visualization of macromolecular structures. By fully adopting capabilities of modern web browsers, such as WebGL, for molecular graphics, the viewer can interactively display large molecular complexes and is also unaffected by the retirement of third-party plug-ins like Flash and Java Applets. Generally, the web application offers comprehensive molecular visualization through a graphical user interface so that life scientists can easily access and profit from available structural data. It supports common structural file-formats (e.g. PDB, mmCIF) and a variety of molecular representations (e.g. 'cartoon, spacefill, licorice'). Moreover, the viewer can be embedded in other web sites to provide specialized visualizations of entries in structural databases or results of structure-related calculations.

CyToStruct: Augmenting the Network Visualization of Cytoscape with the Power of Molecular Viewers

It can be informative to view biological data, e.g., protein-protein interactions within a large complex, in a network representation coupled with three-dimensional structural visualizations of individual molecular entities. CyToStruct, introduced here, provides a transparent interface between the Cytoscape platform for network analysis and molecular viewers, including PyMOL, UCSF Chimera, VMD, and Jmol. CyToStruct launches and passes scripts to molecular viewers from the network's edges and nodes. We provide demonstrations to analyze interactions among subunits in large protein/RNA/DNA complexes, and similarities among proteins. CyToStruct enriches the network tools of Cytoscape by adding a layer of structural analysis, offering all capabilities implemented in molecular viewers. CyToStruct is available at https://bitbucket.org/sergeyn/cytostruct/wiki/Home and in the Cytoscape App Store. Given the coordinates of a molecular complex, our web server (http://trachel-srv.cs.haifa.ac.il/rachel/ppi/) automatically generates all files needed to visualize the complex as a Cytoscape network with CyToStruct bridging to PyMOL, UCSF Chimera, VMD, and Jmol.