Interactive 3D Representations Research Articles

A methodological approach for enhancing visualization of country data representation in the presence of significant spatial disparity

In this article, we present a methodological approach to address spatial disparity in global data representation, introducing an algorithm called Flexible Mapping to Understand Spatial Analysis (FLEMUSA). We utilize world maps to depict various data points across countries, revealing substantial variation among them. However, conventional choropleth maps often fail to effectively represent regions with sparse data, obscuring valuable insights. To mitigate this issue, we propose interactive graphical methods in both two and three dimensions, implemented through open-source Python code accessible via Google Colab. Our approach includes several contributions such as excluding countries without data from the representation, scaling magnitudes within country borders, focusing on regional analysis, and using logarithmic scales for bubble maps proportional to country sizes. Additionally, we offer interactive 2D and 3D representations, rotatable 3D representations, and zoomable options, facilitating enhanced visualization of regional similarities amidst data heterogeneity. Through this algorithm, we aim to improve the clarity and interpretability of spatial data analysis, integrating solutions for extreme data overdispersion, all programmed with open-source code.-Utilization of world maps for visual representation of data across countries mitigating the overdispersion step by step.-Implementation of graphical methods, including interactive 2D and 3D maps, to address spatial disparity.-Provision of open-source code for customizable graphical representations, facilitating implementation in online journals as interactive code snippets.

Interactive Human 3D Model with Conventional AI

Abstract: The convergence of interactive human 3D models with conventional artificial intelligence (AI) represents a groundbreaking fusion of computer graphics and intelligent systems. This interdisciplinary field combines advanced 3D modeling techniques with classical AI methodologies to create interactive virtual representations of humans. Rigorous studies in 3D modeling and animation form the basis for lifelike avatars, while conventional AI empowers these models with the ability to understand user inputs, make contextually relevant decisions, and engage in dynamic and responsive interactions. At the heart of this innovation is the emphasis on human-computer interaction (HCI), leveraging principles such as gesture recognition, voice commands, and user-friendly interfaces to enhance user experiences. The integration extends into virtual and augmented reality (VR/AR), providing users with immersive and engaging environments where interactive 3D human models come to life. Applications of this technology span a wide array of fields, including virtual companionship, education, healthcare simulations, entertainment, and training scenarios. The impact is transformative, offering new possibilities for human-machine interactions and redefining traditional approaches to AI applications. However, the burgeoning field is not without challenges. Privacy concerns, ethical considerations related to realistic human representation, and the societal impact of interactive 3D models necessitate careful examination. This abstract provides a glimpse into the technical intricacies of creating lifelike models, the intelligence driving their interactive capabilities, and the broader implications for diverse applications and industries. As research and development progress, the collaboration of computer graphics and AI not only opens new avenues but also prompts a thoughtful reevaluation of the evolving relationship between humans and intelligent, interactive 3D representations.

Preoperative planning using virtual reality and computed tomography angiogram in deep inferior epigastric perforator flap breast reconstruction

The gold standard for preoperative planning of deep inferior epigastric perforator (DIEP) flap breast reconstruction uses computed tomography angiography (CTA). Virtual reality (VR) circumnavigates the limitations of CTA by reconstructing a fully immersive and interactive 3D representation of the scan. Scans of 44 patients who underwent DIEP flap breast reconstruction were retrospectively reviewed and compared using CTA and VR imaging modalities. The objective of this research was to compare perforators found using VR to the ones identified using conventional CTA. A correlation was found between the imaging modalities for unilateral (R = 0.96 (CI = 0.92, 0.98)) and bilateral (R = 0.93, (CI = 0.83, 0.97)) DIEP flap surgeries when comparing perforator location related to the umbilicus. Multivariable ordinal logistic regression found that higher intramuscular course length (IMC) is associated with the number of perforators found per side (OR = 1.79 (CI = 1.24, 2.6)), and medial location (OR = 2.85 (CI = 1.38, 5.87)). Larger vessel caliber (VC) is associated with shorter IMC (T2 vs. T3, OR = 3.34 (CI = 1.49, 7.49)), and branching in adipose tissue (AB) is associated with higher VC (T1 vs. T3, OR = 0.02 (CI = 0.007, 0.08); T2 vs. T3, OR = 0.24 (CI = 0.11, 0.55)). Overall, preoperative planning using VR was easy to use, safe, more intuitive, and provided in a time-efficient manner, more information about perforant characteristics. VR can improve the surgeon’s decision accuracy, relating to the best perforators for harvesting, in a shorter time period.

Use of geodesign tools for visualisation of scenarios for an ecologically sensitive area at a local scale

This study presents methods to create past, recent and alternate scenarios for an ecologically sensitive and development prone area in a sub-tropical coastal spit. A variety of geodesign tools were used for creating interactive 3d representations of the digital earth at a local scale. The geodesign tools included existing and archived high-resolution active and passive remote sensing datasets, existing, derived and digitised spatial layers together with products of procedural modelling. The 3d representations in virtual environments of different scenarios were further converted to a diverse variety of digital formats to enable their visualisation across diverse media that included interactive 3d scenes in geographical information systems (GIS), interactive web scenes on web browsers (desktops and smart devices), fly-through in generic movie formats and real 3d visualisation in the CAVE2 environment. This study discusses the utility of all the resources for planning curriculum and the potential of these resources to facilitate an understanding of alternate scenarios for citizens, stakeholders and new learners. Finally, this study evaluates sources while critically discussing openly shared resources in the context of collaborative planning with citizens, educators, students and planners.

Virtual Loom: a tool for the interactive 3D representation of historical fabrics

3D modelling of man-made objects is widely used in the cultural heritage sector, among others. It is relevant for its documentation, dissemination and preservation. Related to historical fabrics, weaves and weaving techniques are still mostly represented in forms of 2D graphics and textual descriptions. However, complex geometries are difficult to represent in such forms, hindering the way this legacy is transmitted to new generations. In this paper, we present the design and implementation of SILKNOW’s Virtual Loom, an interactive tool aimed to document, preserve and represent in interactive 3D forms historical weaves and weaving techniques of silk fabrics, dating from the 15th to the 19th centuries. To that end, our tool only requires an image of a historical fabric. Departing from this image, the tool automatically subtracts the design, and allows the user to apply different weaves and weaving techniques. In its current version, the tool embeds five traditional weaving techniques, 39 weaves and six types of yarns, which have been defined thanks to close collaboration of experts in computer graphics, art history and historical fabrics. Additionally, users can change the color of yarns and produce different 3D representations for a given fabric, which are interactive in real time. In this paper, we bring the details of the design and implementation of this tool, focusing on the input data, the strategy to process images, the 3D modelling of yarns, the definition of weaves and weaving techniques and the graphical user interface. In the results section, we show some examples of image analysis in order to subtract the design of historical fabrics, and then we provide 3D representations for all the considered weaving techniques, combining different types of yarns.

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Protein alignments are commonly used to evaluate the similarity of protein residues, and the derived consensus sequence used for identifying functional units (e.g., domains). Traditional consensus-building models fail to account for interpositional dependencies – functionally required covariation of residues that tend to appear simultaneously throughout evolution and across the phylogentic tree. These relationships can reveal important clues about the processes of protein folding, thermostability, and the formation of functional sites, which in turn can be used to inform the engineering of synthetic proteins. Unfortunately, these relationships essentially form sub-motifs which cannot be predicted by simple “majority rule” or even HMM-based consensus models, and the result can be a biologically invalid “consensus” which is not only never seen in nature but is less viable than any extant protein. We have developed a visual analytics tool, StickWRLD, which creates an interactive 3D representation of a protein alignment and clearly displays covarying residues. The user has the ability to pan and zoom, as well as dynamically change the statistical threshold underlying the identification of covariants. StickWRLD has previously been successfully used to identify functionally-required covarying residues in proteins such as Adenylate Kinase and in DNA sequences such as endonuclease target sites.

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues.

Protein alignments are commonly used to evaluate the similarity of protein residues, and the derived consensus sequence used for identifying functional units (e.g., domains). Traditional consensus-building models fail to account for interpositional dependencies – functionally required covariation of residues that tend to appear simultaneously throughout evolution and across the phylogentic tree. These relationships can reveal important clues about the processes of protein folding, thermostability, and the formation of functional sites, which in turn can be used to inform the engineering of synthetic proteins. Unfortunately, these relationships essentially form sub-motifs which cannot be predicted by simple “majority rule” or even HMM-based consensus models, and the result can be a biologically invalid “consensus” which is not only never seen in nature but is less viable than any extant protein. We have developed a visual analytics tool, StickWRLD, which creates an interactive 3D representation of a protein alignment and clearly displays covarying residues. The user has the ability to pan and zoom, as well as dynamically change the statistical threshold underlying the identification of covariants. StickWRLD has previously been successfully used to identify functionally-required covarying residues in proteins such as Adenylate Kinase and in DNA sequences such as endonuclease target sites.

Interactions between continent-like ‘drift’, rifting and mantle flow on Venus: gravity interpretations and Earth analogues

Abstract Regional shear zones are interpreted from Bouguer gravity data over northern polar to low southern latitudes of Venus. Offset and deflection of horizontal gravity gradient edges (‘worms’) and lineaments interpreted from displacement of Bouguer anomalies portray crustal structures, the geometry of which resembles both regional transcurrent shear zones bounding or cross-cutting cratons and fracture zones in oceanic crust on Earth. High Bouguer anomalies and thinned crust comparable to the Mid-Continent Rift in North America suggest underplating of denser, mantle-derived mafic material beneath extended crust in Sedna and Guinevere planitia on Venus. These rifts are partitioned by transfer faults and flank a zone of mantle upwelling (Eistla Regio) between colinear hot, upwelling mantle plumes. Data support the northward drift and indentation of Lakshmi Planum in western Ishtar Terra and >1000 km of transcurrent displacement between Ovda and Thetis regiones. Large displacements of areas of continent-like crust on Venus are interpreted to result from mantle tractions and pressure acting against their deep lithospheric mantle ‘keels’ commensurate with extension in adjacent rifts. Displacements of Lakshmi Planum and Ovda and Thetis regiones on Venus, a planet without plate tectonics, cannot be attributed to plate boundary forces (i.e. ridge push and slab pull). Results therefore suggest that a similar, subduction-free geodynamic model may explain deformation features in Archaean greenstone terrains on Earth. Continent-like ‘drift’ on Venus also resembles models for the late Cenozoic–Recent Earth, where westward translation of the Americas and northward displacement of India are interpreted as being driven by mantle flow tractions on the keels of their Precambrian cratons. Supplementary material: Bouguer gravity and topographic images over a segment of the Mid-Atlantic ridge and Ross Island and surrounds in Antarctica, principal horizontal stress trajectories about mantle plumes on Earth, map and interactive 3D representations of cratonic keels beneath North America from seismic tomography, and a centrifuge simulation for comparison with Venus in support of our tectonic model are available at http://www.geolsoc.org.uk/SUP18736 .

Oligomeric Structure of the MALT1 Tandem Ig-Like Domains

BackgroundMucosa-associated lymphoid tissue 1 (MALT1) plays an important role in the adaptive immune program. During TCR- or BCR-induced NF-κB activation, MALT1 serves to mediate the activation of the IKK (IκB kinase) complex, which subsequently regulates the activation of NF-κB. Aggregation of MALT1 is important for E3 ligase activation and NF-κB signaling.Principal FindingsUnlike the isolated CARD or paracaspase domains, which behave as monomers, the tandem Ig-like domains of MALT1 exists as a mixture of dimer and tetramer in solution. High-resolution structures reveals a protein-protein interface that is stabilized by a buried surface area of 1256 Å2 and contains numerous hydrogen and salt bonds. In conjunction with a second interface, these interactions may represent the basis of MALT1 oligomerization.ConclusionsThe crystal structure of the tandem Ig-like domains reveals the oligomerization potential of MALT1 and a potential intermediate in the activation of the adaptive inflammatory pathway.Enhanced version This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1.

Characterization of 14-3-3 Proteins from Cryptosporidium parvum

The parasite Cryptosporidium parvum has three 14-3-3 proteins: Cp14ε, Cp14a and Cp14b, with only Cp14ε similar to human 14-3-3 proteins in sequence, peptide-binding properties and structure. Structurally, Cp14a features the classical 14-3-3 dimer but with a uniquely wide pocket and a disoriented RRY triad potentially incapable of binding phosphopeptides. The Cp14b protein deviates from the norm significantly: (i) In one subunit, the phosphorylated C-terminal tail is bound in the binding groove like a phosphopeptide. This supports our binding study indicating this protein was stabilized by a peptide mimicking its last six residues. (ii) The other subunit has eight helices instead of nine, with αA and αB forming a single helix and occluding the peptide-binding cleft. (iii) The protein forms a degenerate dimer with the two binding grooves divided and facing opposite directions. These features conspire to block and disrupt the bicameral substrate-binding pocket, suggesting a possible tripartite auto-regulation mechanism that has not been observed previously.Enhanced version This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1.

Comparative Structural Analysis of Lipid Binding START Domains

BackgroundSteroidogenic acute regulatory (StAR) protein related lipid transfer (START) domains are small globular modules that form a cavity where lipids and lipid hormones bind. These domains can transport ligands to facilitate lipid exchange between biological membranes, and they have been postulated to modulate the activity of other domains of the protein in response to ligand binding. More than a dozen human genes encode START domains, and several of them are implicated in a disease.Principal FindingsWe report crystal structures of the human STARD1, STARD5, STARD13 and STARD14 lipid transfer domains. These represent four of the six functional classes of START domains.SignificanceSequence alignments based on these and previously reported crystal structures define the structural determinants of human START domains, both those related to structural framework and those involved in ligand specificity.Enhanced version This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1.

Structural and Histone Binding Ability Characterizations of Human PWWP Domains

BackgroundThe PWWP domain was first identified as a structural motif of 100–130 amino acids in the WHSC1 protein and predicted to be a protein-protein interaction domain. It belongs to the Tudor domain ‘Royal Family’, which consists of Tudor, chromodomain, MBT and PWWP domains. While Tudor, chromodomain and MBT domains have long been known to bind methylated histones, PWWP was shown to exhibit histone binding ability only until recently.Methodology/Principal FindingsThe PWWP domain has been shown to be a DNA binding domain, but sequence analysis and previous structural studies show that the PWWP domain exhibits significant similarity to other ‘Royal Family’ members, implying that the PWWP domain has the potential to bind histones. In order to further explore the function of the PWWP domain, we used the protein family approach to determine the crystal structures of the PWWP domains from seven different human proteins. Our fluorescence polarization binding studies show that PWWP domains have weak histone binding ability, which is also confirmed by our NMR titration experiments. Furthermore, we determined the crystal structures of the BRPF1 PWWP domain in complex with H3K36me3, and HDGF2 PWWP domain in complex with H3K79me3 and H4K20me3.ConclusionsPWWP proteins constitute a new family of methyl lysine histone binders. The PWWP domain consists of three motifs: a canonical β-barrel core, an insertion motif between the second and third β-strands and a C-terminal α-helix bundle. Both the canonical β-barrel core and the insertion motif are directly involved in histone binding. The PWWP domain has been previously shown to be a DNA binding domain. Therefore, the PWWP domain exhibits dual functions: binding both DNA and methyllysine histones.Enhanced version This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1.

Structural studies of the tandem Tudor domains of fragile X mental retardation related proteins FXR1 and FXR2.

BackgroundExpansion of the CGG trinucleotide repeat in the 5′-untranslated region of the FMR1, fragile X mental retardation 1, gene results in suppression of protein expression for this gene and is the underlying cause of Fragile X syndrome. In unaffected individuals, the FMRP protein, together with two additional paralogues (Fragile X Mental Retardation Syndrome-related Protein 1 and 2), associates with mRNA to form a ribonucleoprotein complex in the nucleus that is transported to dendrites and spines of neuronal cells. It is thought that the fragile X family of proteins contributes to the regulation of protein synthesis at sites where mRNAs are locally translated in response to stimuli.Methodology/Principal FindingsHere, we report the X-ray crystal structures of the non-canonical nuclear localization signals of the FXR1 and FXR2 autosomal paralogues of FMRP, which were determined at 2.50 and 1.92 Å, respectively. The nuclear localization signals of the FXR1 and FXR2 comprise tandem Tudor domain architectures, closely resembling that of UHRF1, which is proposed to bind methylated histone H3K9.ConclusionsThe FMRP, FXR1 and FXR2 proteins comprise a small family of highly conserved proteins that appear to be important in translational regulation, particularly in neuronal cells. The crystal structures of the N-terminal tandem Tudor domains of FXR1 and FXR2 revealed a conserved architecture with that of FMRP. Biochemical analysis of the tandem Tudor doamins reveals their ability to preferentially recognize trimethylated peptides in a sequence-specific manner.Enhanced version This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1.

High-Affinity Inhibitors of Human NAD+-Dependent 15-Hydroxyprostaglandin Dehydrogenase: Mechanisms of Inhibition and Structure-Activity Relationships

Background15-hydroxyprostaglandin dehydrogenase (15-PGDH, EC 1.1.1.141) is the key enzyme for the inactivation of prostaglandins, regulating processes such as inflammation or proliferation. The anabolic pathways of prostaglandins, especially with respect to regulation of the cyclooxygenase (COX) enzymes have been studied in detail; however, little is known about downstream events including functional interaction of prostaglandin-processing and -metabolizing enzymes. High-affinity probes for 15-PGDH will, therefore, represent important tools for further studies.Principal FindingsTo identify novel high-affinity inhibitors of 15-PGDH we performed a quantitative high-throughput screen (qHTS) by testing >160 thousand compounds in a concentration-response format and identified compounds that act as noncompetitive inhibitors as well as a competitive inhibitor, with nanomolar affinity. Both types of inhibitors caused strong thermal stabilization of the enzyme, with cofactor dependencies correlating with their mechanism of action. We solved the structure of human 15-PGDH and explored the binding modes of the inhibitors to the enzyme in silico. We found binding modes that are consistent with the observed mechanisms of action.ConclusionsLow cross-reactivity in screens of over 320 targets, including three other human dehydrogenases/reductases, suggest selectivity of the present inhibitors for 15-PGDH. The high potencies and different mechanisms of action of these chemotypes make them a useful set of complementary chemical probes for functional studies of prostaglandin-signaling pathways.Enhanced version This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S2.

The Crystal Structure of the Dachshund Domain of Human SnoN Reveals Flexibility in the Putative Protein Interaction Surface

The human SnoN is an oncoprotein that interacts with several transcription-regulatory proteins such as the histone-deacetylase, N-CoR containing co-repressor complex and Smad proteins. This study presents the crystal structure of the Dachshund homology domain of human SnoN. The structure reveals a groove composed of conserved residues with characteristic properties of a protein-interaction surface. A comparison of the 12 monomers in the asymmetric unit reveals the presence of two major conformations: an open conformation with a well accessible groove and a tight conformation with a less accessible groove. The variability in the backbone between the open and the tight conformations matches the differences seen in previously determined structures of individual Dachshund homology domains, suggesting a general plasticity within this fold family. The flexibility observed in the putative protein binding groove may enable SnoN to recognize multiple interaction partners.Enhanced version This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1.

The Crystal Structure of Toxoplasma gondii Pyruvate Kinase 1

BackgroundPyruvate kinase (PK), which catalyzes the final step in glycolysis converting phosphoenolpyruvate to pyruvate, is a central metabolic regulator in most organisms. Consequently PK represents an attractive therapeutic target in cancer and human pathogens, like Apicomplexans. The phylum Aplicomplexa, a group of exclusively parasitic organisms, includes the genera Plasmodium, Cryptosporidium and Toxoplasma, the etiological agents of malaria, cryptosporidiosis and toxoplasmosis respectively. Toxoplasma gondii infection causes a mild illness and is a very common infection affecting nearly one third of the world's population.Methodology/Principal FindingsWe have determined the crystal structure of the PK1 enzyme from T. gondii, with the B domain in the open and closed conformations. We have also characterized its enzymatic activity and confirmed glucose-6-phosphate as its allosteric activator. This is the first description of a PK enzyme in a closed inactive conformation without any bound substrate. Comparison of the two tetrameric TgPK1 structures indicates a reorientation of the monomers with a concomitant change in the buried surface among adjacent monomers. The change in the buried surface was associated with significant B domain movements in one of the interacting monomers.ConclusionsWe hypothesize that a loop in the interface between the A and B domains plays an important role linking the position of the B domain to the buried surface among monomers through two α-helices. The proposed model links the catalytic cycle of the enzyme with its domain movements and highlights the contribution of the interface between adjacent subunits. In addition, an unusual ordered conformation was observed in one of the allosteric binding domains and it is related to a specific apicomplexan insertion. The sequence and structural particularity would explain the atypical activation by a mono-phosphorylated sugar. The sum of peculiarities raises this enzyme as an emerging target for drug discovery.Enhanced version This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1.

Structural Comparison of Human Mammalian Ste20-Like Kinases

BackgroundThe serine/threonine mammalian Ste-20 like kinases (MSTs) are key regulators of apoptosis, cellular proliferation as well as polarization. Deregulation of MSTs has been associated with disease progression in prostate and colorectal cancer. The four human MSTs are regulated differently by C-terminal regions flanking the catalytic domains.Principal FindingsWe have determined the crystal structure of kinase domain of MST4 in complex with an ATP-mimetic inhibitor. This is the first structure of an inactive conformation of a member of the MST kinase family. Comparison with active structures of MST3 and MST1 revealed a dimeric association of MST4 suggesting an activation loop exchanged mechanism of MST4 auto-activation. Together with a homology model of MST2 we provide a comparative analysis of the kinase domains for all four members of the human MST family.SignificanceThe comparative analysis identified new structural features in the MST ATP binding pocket and has also defined the mechanism for autophosphorylation. Both structural features may be further explored for inhibitors design.Enhanced version This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1.

VmdICE: A plug‐in for rapid evaluation of molecular dynamics simulations using VMD

Molecular dynamics (MD) is a powerful in silico method to investigate the interactions between biomolecules. It solves Newton's equations of motion for atoms over a specified period of time and yields a trajectory file, containing the different spatial arrangements of atoms during the simulation. The movements and energies of each single atom are recorded. For evaluating of these simulation trajectories with regard to biomedical implications, several methods are available. Three well-known ones are the root mean square deviation (RMSD), the root mean square fluctuation (RMSF) and solvent accessible surface area (SASA). Herein, we present a novel plug-in for the software "visual molecular dynamics" (VMD) that allows an interactive 3D representation of RMSD, RMSF, and SASA, directly on the molecule. On the one hand, our plug-in is easy to handle for inexperienced users, and on the other hand, it provides a fast and flexible graphical impression of the spatial dynamics of a system for experts in the field.

The Virtual Point 1 event display for the ATLAS experiment

We present an event display for the ATLAS Experiment, called Virtual Point 1 (VP1), designed initially for deployment at point 1 of the LHC, the location of the ATLAS detector. The Qt/OpenGL based application provides truthful and interactive 3D representations of both event and non-event data, and now serves a general-purpose role within the experiment. Thus, VP1 is used both online (in the control room itself or remotely via a special "live" mode) and offline environments to provide fast debugging and understanding of events, detector status and software. In addition to a flexible plugin infrastructure and a high level of configurability, this multi-purpose role is mainly facilitated by embedding the application directly into the ATLAS offline software framework, enabling it to use the native Event Data Model directly, and thus run on any source of ATLAS data, or even directly from within processes such as reconstruction jobs. Finally, VP1 provides high-quality pictures and movies, useful for outreach purposes.

Structural Biology of Human H3K9 Methyltransferases

SET domain methyltransferases deposit methyl marks on specific histone tail lysine residues and play a major role in epigenetic regulation of gene transcription. We solved the structures of the catalytic domains of GLP, G9a, Suv39H2 and PRDM2, four of the eight known human H3K9 methyltransferases in their apo conformation or in complex with the methyl donating cofactor, and peptide substrates. We analyzed the structural determinants for methylation state specificity, and designed a G9a mutant able to tri-methylate H3K9. We show that the I-SET domain acts as a rigid docking platform, while induced-fit of the Post-SET domain is necessary to achieve a catalytically competent conformation. We also propose a model where long-range electrostatics bring enzyme and histone substrate together, while the presence of an arginine upstream of the target lysine is critical for binding and specificity.Enhanced version This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1.