Structural predictions of protein-DNA binding: MELD-DNA.

Structural, regulatory and enzymatic proteins interact with DNA to maintain a healthy and functional genome. Yet, our structural understanding of how proteins interact with DNA is limited. We present MELD-DNA, a novel computational approach to predict the structures of protein-DNA complexes. The method combines molecular dynamics simulations with general knowledge or experimental information through Bayesian inference. The physical model is sensitive to sequence-dependent properties and conformational changes required for binding, while information accelerates sampling of bound conformations. MELD-DNA can: (i) sample multiple binding modes; (ii) identify the preferred binding mode from the ensembles; and (iii) provide qualitative binding preferences between DNA sequences. We first assess performance on a dataset of 15 protein-DNA complexes and compare it with state-of-the-art methodologies. Furthermore, for three selected complexes, we show sequence dependence effects of binding in MELD predictions. We expect that the results presented herein, together with the freely available software, will impact structural biology (by complementing DNA structural databases) and molecular recognition (by bringing new insights into aspects governing protein-DNA interactions).

An overload of missense variants in the OTOG gene may drive a higher prevalence of familial Meniere disease in the European population.

Meniere disease is a complex inner ear disorder with significant familial aggregation. A differential prevalence of familial MD (FMD) has been reported, being 9-10% in Europeans compared to 6% in East Asians. A broad genetic heterogeneity in FMD has been described, OTOG being the most common mutated gene, with a compound heterozygous recessive inheritance. We hypothesize that an OTOG-related founder effect may explain the higher prevalence of FMD in the European population. Therefore, the present study aimed to compare the allele frequency (AF) and distribution of OTOG rare variants across different populations. For this purpose, the coding regions with high constraint (low density of rare variants) were retrieved in the OTOG coding sequence in Non-Finnish European (NFE).. Missense variants (AF < 0.01) were selected from a 100 FMD patient cohort, and their population AF was annotated using gnomAD v2.1. A linkage analysis was performed, and odds ratios were calculated to compare AF between NFE and other populations. Thirteen rare missense variants were observed in 13 FMD patients, with 2 variants (rs61978648 and rs61736002) shared by 5 individuals and another variant (rs117315845) shared by two individuals. The results confirm the observed enrichment of OTOG rare missense variants in FMD. Furthermore, eight variants were enriched in the NFE population, and six of them were in constrained regions. Structural modeling predicts five missense variants that could alter the otogelin stability. We conclude that several variants reported in FMD are in constraint regions, and they may have a founder effect and explain the burden of FMD in the European population.

Structural Elucidation of Ubiquitin via Gas-Phase Ion/Ion Cross-Linking Reactions Using Sodium-Cationized Reagents Coupled with Infrared Multiphoton Dissociation.

Accurate structural determination of proteins is critical to understanding their biological functions and the impact of structural disruption on disease progression. Gas-phase cross-linking mass spectrometry (XL-MS) via ion/ion reactions between multiply charged protein cations and singly charged cross-linker anions has previously been developed to obtain low-resolution structural information on proteins. This method significantly shortens experimental time relative to conventional solution-phase XL-MS but has several technical limitations: (1) the singly deprotonated N-hydroxysulfosuccinimide (sulfo-NHS)-based cross-linker anions are restricted to attachment at neutral amine groups of basic amino acid residues and (2) analyzing terminal cross-linked fragment ions is insufficient to unambiguously localize sites of linker attachment. Herein, we demonstrate enhanced structural information for alcohol-denatured A-state ubiquitin obtained from an alternative gas-phase XL-MS approach. Briefly, singly sodiated ethylene glycol bis(sulfosuccinimidyl succinate) (sulfo-EGS) cross-linker anions enable covalent cross-linking at both ammonium and amine groups. Additionally, covalently modified internal fragment ions, along with terminal b-/y-type counterparts, improve the determination of linker attachment sites. Molecular dynamics simulations validate experimentally obtained gas-phase conformations of denatured ubiquitin. This method has identified four cross-linking sites across 8+ ubiquitin, including two new sites in the N-terminal region of the protein that were originally inaccessible in prior gas-phase XL approaches. The two N-terminal cross-linking sites suggest that the N-terminal half of ubiquitin is more compact in gas-phase conformations. By comparison, the two C-terminal linker sites indicate the signature transformation of this region of the protein from a native to a denatured conformation. Overall, the results suggest that the solution-phase secondary structures of the A-state ubiquitin are conserved in the gas phase. This method also provides sufficient sensitivity to differentiate between two gas-phase conformers of the same charge state with subtle structural variations.

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge.

This paper describes outcomes of the 2019 Cryo-EM Model Challenge. The goals were to (1) assess the quality of models that can be produced from cryogenic electron microscopy (cryo-EM) maps using current modeling software, (2) evaluate reproducibility of modeling results from different software developers and users and (3) compare performance of current metrics used for model evaluation, particularly Fit-to-Map metrics, with focus on near-atomic resolution. Our findings demonstrate the relatively high accuracy and reproducibility of cryo-EM models derived by 13 participating teams from four benchmark maps, including three forming a resolution series (1.8 to 3.1 Å). The results permit specific recommendations to be made about validating near-atomic cryo-EM structures both in the context of individual experiments and structure data archives such as the Protein Data Bank. We recommend the adoption of multiple scoring parameters to provide full and objective annotation and assessment of the model, reflective of the observed cryo-EM map density.

GENERALIST: A latent space based generative model for protein sequence families.

Generative models of protein sequence families are an important tool in the repertoire of protein scientists and engineers alike. However, state-of-the-art generative approaches face inference, accuracy, and overfitting- related obstacles when modeling moderately sized to large proteins and/or protein families with low sequence coverage. Here, we present a simple to learn, tunable, and accurate generative model, GENERALIST: GENERAtive nonLInear tenSor-factorizaTion for protein sequences. GENERALIST accurately captures several high order summary statistics of amino acid covariation. GENERALIST also predicts conservative local optimal sequences which are likely to fold in stable 3D structure. Importantly, unlike current methods, the density of sequences in GENERALIST-modeled sequence ensembles closely resembles the corresponding natural ensembles. Finally, GENERALIST embeds protein sequences in an informative latent space. GENERALIST will be an important tool to study protein sequence variability.

Etiological diagnosis of recurrent acute pancreatitis.

Acute pancreatitis is the leading cause of inpatient care among gastrointestinal conditions. Despite early intervention, one-third of patients experience recurrent acute pancreatitis (RAP). A comprehensive diagnostic approach is warranted to identify and treat underlying factors in order to prevent recurrence. RAP is most frequent among men aged 30-40, smokers, and in those with excessive alcohol consumption. To identify the etiology is paramount to stratify patients according to their individual risk of RAP and for predicting an eventual evolution to chronic pancreatitis. Although the initial management of acute pancreatitis is widely homogeneous according to established guidelines, there are no defined protocols to investigate RAP. In the present editorial article we propose a structured algorithm with precise recommendations to investigate the etiology RAP as part of routine clinical practice. Although there are relevant knowledge gaps in this disease, we believe that our guidance would contribute for a more homogenous diagnostic approach of RAP in clinical practice.

A Computational Pipeline for Accurate Prioritization of Protein-Protein Binding Candidates in High-Throughput Protein Libraries.

Identifying the interactome for a protein of interest is challenging due to the large number of possible binders. High-throughput experimental approaches narrow down possible binding partners but often include false positives. Furthermore, they provide no information about what the binding region is (e.g., the binding epitope). We introduce a novel computational pipeline based on an AlphaFold2 (AF) Competitive Binding Assay (AF-CBA) to identify proteins that bind a target of interest from a pull-down experiment and the binding epitope. Our focus is on proteins that bind the Extraterminal (ET) domain of Bromo and Extraterminal domain (BET) proteins, but we also introduce nine additional systems to show transferability to other peptide-protein systems. We describe a series of limitations to the methodology based on intrinsic deficiencies of AF and AF-CBA to help users identify scenarios where the approach will be most useful. Given the method's speed and accuracy, we anticipate its broad applicability to identify binding epitope regions among potential partners, setting the stage for experimental verification.

Automated Deep Learning Artificial Intelligence Tool for Spleen Segmentation on CT: Defining Volume-Based Thresholds for Splenomegaly.

BACKGROUND. Splenomegaly historically has been assessed on imaging by use of potentially inaccurate linear measurements. Prior work tested a deep learning artificial intelligence (AI) tool that automatically segments the spleen to determine splenic volume. OBJECTIVE. The purpose of this study is to apply the deep learning AI tool in a large screening population to establish volume-based splenomegaly thresholds. METHODS. This retrospective study included a primary (screening) sample of 8901 patients (4235 men, 4666 women; mean age, 56 ± 10 [SD] years) who underwent CT colonoscopy (n = 7736) or renal donor CT (n = 1165) from April 2004 to January 2017 and a secondary sample of 104 patients (62 men, 42 women; mean age, 56 ± 8 years) with end-stage liver disease who underwent contrast-enhanced CT performed as part of evaluation for potential liver transplant from January 2011 to May 2013. The automated deep learning AI tool was used for spleen segmentation, to determine splenic volumes. Two radiologists independently reviewed a subset of segmentations. Weight-based volume thresholds for splenomegaly were derived using regression analysis. Performance of linear measurements was assessed. Frequency of splenomegaly in the secondary sample was determined using weight-based volumetric thresholds. RESULTS. In the primary sample, both observers confirmed splenectomy in 20 patients with an automated splenic volume of 0 mL; confirmed incomplete splenic coverage in 28 patients with a tool output error; and confirmed adequate segmentation in 21 patients with low volume (< 50 mL), 49 patients with high volume (> 600 mL), and 200 additional randomly selected patients. In 8853 patients included in analysis of splenic volumes (i.e., excluding a value of 0 mL or error values), the mean automated splenic volume was 216 ± 100 [SD] mL. The weight-based volumetric threshold (expressed in milliliters) for splenomegaly was calculated as (3.01 × weight [expressed as kilograms]) + 127; for weight greater than 125 kg, the splenomegaly threshold was constant (503 mL). Sensitivity and specificity for volume-defined splenomegaly were 13% and 100%, respectively, at a true craniocaudal length of 13 cm, and 78% and 88% for a maximum 3D length of 13 cm. In the secondary sample, both observers identified segmentation failure in one patient. The mean automated splenic volume in the 103 remaining patients was 796 ± 457 mL; 84% (87/103) of patients met the weight-based volume-defined splenomegaly threshold. CONCLUSION. We derived a weight-based volumetric threshold for splenomegaly using an automated AI-based tool. CLINICAL IMPACT. The AI tool could facilitate large-scale opportunistic screening for splenomegaly.

Utility of Fully Automated Body Composition Measures on Pretreatment Abdominal CT for Predicting Survival in Patients With Colorectal Cancer.

BACKGROUND. CT examinations contain opportunistic body composition data with potential prognostic utility. Previous studies have primarily used manual or semiautomated tools to evaluate body composition in patients with colorectal cancer (CRC). OBJECTIVE. The purpose of this article is to assess the utility of fully automated body composition measures derived from pretreatment CT examinations in predicting survival in patients with CRC. METHODS. This retrospective study included 1766 patients (mean age, 63.7 ± 14.4 [SD] years; 862 men, 904 women) diagnosed with CRC between January 2001 and September 2020 who underwent pretreatment abdominal CT. A panel of fully automated artificial intelligence-based algorithms was applied to portal venous phase images to quantify skeletal muscle attenuation at the L3 lumbar level, visceral adipose tissue (VAT) area and subcutaneous adipose tissue (SAT) area at L3, and abdominal aorta Agatston score (aortic calcium). The electronic health record was reviewed to identify patients who died of any cause (n = 848). ROC analyses and logistic regression analyses were used to identify predictors of survival, with attention to highest- and lowest-risk quartiles. RESULTS. Patients who died, compared with patients who survived, had lower median muscle attenuation (19.2 vs 26.2 HU, p < .001), SAT area (168.4 cm2 vs 197.6 cm2, p < .001), and aortic calcium (620 vs 182, p < .001). Measures with highest 5-year AUCs for predicting survival in patients without (n = 1303) and with (n = 463) metastatic disease were muscle attenuation (0.666 and 0.701, respectively) and aortic calcium (0.677 and 0.689, respectively). A combination of muscle attenuation, SAT area, and aortic calcium yielded 5-year AUCs of 0.758 and 0.732 in patients without and with metastases, respectively. Risk of death was increased (p < .05) in patients in the lowest quartile for muscle attenuation (hazard ratio [HR] = 1.55) and SAT area (HR = 1.81) and in the highest quartile for aortic calcium (HR = 1.37) and decreased (p < .05) in patients in the highest quartile for VAT area (HR = 0.79) and SAT area (HR = 0.76). In 423 patients with available BMI, BMI did not significantly predict death (p = .75). CONCLUSION. Fully automated CT-based body composition measures including muscle attenuation, SAT area, and aortic calcium predict survival in patients with CRC. CLINICAL IMPACT. Routine pretreatment body composition evaluation could improve initial risk stratification of patients with CRC.

Computational Study of Driving Forces in ATSP, PDIQ, and P53 Peptide Binding: C═O···C═O Tetrel Bonding Interactions at Work.

Understanding the molecular interactions that drive peptide folding is crucial to chemistry and biology. In this study, we analyzed the role of CO···CO tetrel bonding (TtB) interactions in the folding mechanism of three different peptides (ATSP, pDIQ, and p53), which exhibit a different propensity to fold in an α helix motif. To achieve this goal, we used both a recently developed Bayesian inference approach (MELDxMD) and Quantum Mechanics (QM) calculations at the RI-MP2/def2-TZVP level of theory. These techniques allowed us to study the folding process and to evaluate the strength of the CO···CO TtBs as well as the synergies between TtBs and hydrogen-bonding (HB) interactions. We believe that the results derived from our study will be helpful for those scientists working in computational biology, peptide chemistry, and structural biology.

Structure Determination of Challenging Protein-Peptide Complexes Combining NMR Chemical Shift Data and Molecular Dynamics Simulations.

Intrinsically disordered regions of proteins often mediate important protein-protein interactions. However, the folding-upon-binding nature of many polypeptide-protein interactions limits the ability of modeling tools to predict the three-dimensional structures of such complexes. To address this problem, we have taken a tandem approach combining NMR chemical shift data and molecular simulations to determine the structures of peptide-protein complexes. Here, we use the MELD (Modeling Employing Limited Data) technique applied to polypeptide complexes formed with the extraterminal domain (ET) of bromo and extraterminal domain (BET) proteins, which exhibit a high degree of binding plasticity. This system is particularly challenging as the binding process includes allosteric changes across the ET receptor upon binding, and the polypeptide binding partners can adopt different conformations (e.g., helices and hairpins) in the complex. In a blind study, the new approach successfully modeled bound-state conformations and binding poses, using only protein receptor backbone chemical shift data, in excellent agreement with experimentally determined structures for moderately tight (Kd ∼100 nM) binders. The hybrid MELD + NMR approach required additional peptide ligand chemical shift data for weaker (Kd ∼250 µM) peptide binding partners. AlphaFold also successfully predicts the structures of some of these peptide-protein complexes. However, whereas AlphaFold can provide qualitative peptide rankings, MELD can directly estimate relative binding affinities. The hybrid MELD + NMR approach offers a powerful new tool for structural analysis of protein-polypeptide complexes involving disorder-to-order transitions upon complex formation, which are not successfully modeled with most other complex prediction methods, providing both the 3D structures of peptide-protein complexes and their relative binding affinities.

AwarNS: A framework for developing context-aware reactive mobile applications for health and mental health.

In recent years, interest and investment in health and mental health smartphone apps have grown significantly. However, this growth has not been followed by an increase in quality and the incorporation of more advanced features in such applications. This can be explained by an expanding fragmentation of existing mobile platforms along with more restrictive privacy and battery consumption policies, with a consequent higher complexity of developing such smartphone applications. To help overcome these barriers, there is a need for robust, well-designed software development frameworks which are designed to be reliable, power-efficient and ethical with respect to data collection practices, and which support the sense-analyse-act paradigm typically employed in reactive mHealth applications. In this article, we present the AwarNS Framework, a context-aware modular software development framework for Android smartphones, which facilitates transparent, reliable, passive and active data sampling running in the background (sense), on-device and server-side data analysis (analyse), and context-aware just-in-time offline and online intervention capabilities (act). It is based on the principles of versatility, reliability, privacy, reusability, and testability. It offers built-in modules for capturing smartphone and associated wearable sensor data (e.g. IMU sensors, geolocation, Wi-Fi and Bluetooth scans, physical activity, battery level, heart rate), analysis modules for data transformation, selection and filtering, performing geofencing analysis and machine learning regression and classification, and act modules for persistence and various notification deliveries. We describe the framework's design principles and architecture design, explain its capabilities and implementation, and demonstrate its use at the hand of real-life case studies implementing various mobile interventions for different mental disorders used in clinical practice.

CryoFold 2.0: Cryo-EM Structure Determination with MELD.

Cryo-electron microscopy data are becoming more prevalent and accessible at higher resolution levels, leading to the development of new computational tools to determine the atomic structure of macromolecules. However, while existing tools adapted from X-ray crystallography are suitable for the highest-resolution maps, new tools are needed for lower-resolution levels and to account for map heterogeneity. In this article, we introduce CryoFold 2.0, an integrative physics-based approach that combines Bayesian inference and the ability to handle multiple data sources with the molecular dynamics flexible fitting (MDFF) approach to determine the structures of macromolecules by using cryo-EM data. CryoFold 2.0 is incorporated into the MELD (modeling employing limited data) plugin, resulting in a pipeline that is more computationally efficient and accurate than running MELD or MDFF alone. The approach requires fewer computational resources and shorter simulation times than the original CryoFold, and it minimizes manual intervention. We demonstrate the effectiveness of the approach on eight different systems, highlighting its various benefits.

Mapping trust relationships in organ donation and transplantation: a conceptual model.

The organ donation and transplantation (ODT) system heavily relies on the willingness of individuals to donate their organs. While it is widely believed that public trust plays a crucial role in shaping donation rates, the empirical support for this assumption remains limited. In order to bridge this knowledge gap, this article takes a foundational approach by elucidating the concept of trust within the context of ODT. By examining the stakeholders involved, identifying influential factors, and mapping the intricate trust relationships among trustors, trustees, and objects of trust, we aim to provide a comprehensive understanding of trust dynamics in ODT. We employ maps and graphs to illustrate the functioning of these trust relationships, enabling a visual representation of the complex interactions within the ODT system. Through this conceptual groundwork, we pave the way for future empirical research to investigate the link between trust and organ donation rates, informed by a clarified understanding of trust in ODT. This study can also provide valuable insights to inform interventions and policies aimed at enhancing organ donation rates.

Plasmodium vivax apical membrane antigen 1I-II from Nicaragua (2012-2013): genetic and antigenic polymorphism.

OBJECTIVE: Genetic and antigenic polymorphism of P. vivax apical membrane antigen-1 (pvama1I-II) from Nicaragua was examined. MATERIALS AND METHODS: Infected blood samples from patients were obtained during 2012-2013. A gene fragment comprising domains I-II was amplified and sequenced, and the genetic parameters, haplotype relationships, genetic structure, and amino acid variation in predicted B cell epitopes were analyzed. RESULTS: 65 sequences of pvama1III had 19 nonsynonymous and five synonymous nucleotide changes. Nicaraguan parasites had low diversity, high linkage disequilibrium, and few recombination events. Neutrality tests indicate a positive and divergent selection, and three genetic clusters with loss of haplotypes were demonstrated. Amino acid variation predominated in predicted B cell epitopes and was closely related to that in Latin American parasites. CONCLUSIONS: Nicaraguan P. vivax is a moderately differentiated population under contraction and focalization processes, and the antigenic diversity resembles that of Latin American parasites. This information is relevant for vaccine development and epidemiological surveillance.

Inconsistency between the Circulatory and the Brain Criteria of Death in the Uniform Determination of Death Act.

The Uniform Determination of Death Act (UDDA) provides that "an individual who has sustained either (1) irreversible cessation of circulatory and respiratory functions or (2) irreversible cessation of all functions of the entire brain, including the brain stem, is dead." We show that the UDDA contains two conflicting interpretations of the phrase "cessation of functions." By one interpretation, what matters for the determination of death is the cessation of spontaneous functions only, regardless of their generation by artificial means. By the other, what matters is the cessation of both spontaneous and artificially supported functions. Because each UDDA criterion uses a different interpretation, the law is conceptually inconsistent. A single consistent interpretation would lead to the conclusion that conscious individuals whose respiratory and circulatory functions are artificially supported are actually dead, or that individuals whose brain is entirely and irreversibly destroyed may be alive. We explore solutions to mitigate the inconsistency.

Ranking Peptide Binders by Affinity with AlphaFold.

AlphaFold has revolutionized structural biology by predicting highly accurate structures of proteins and their complexes with peptides and other proteins. However, for protein-peptide systems, we are also interested in identifying the highest affinity binder among a set of candidate peptides. We present a novel competitive binding assay using AlphaFold to predict structures of the receptor in the presence of two peptides. For systems in which the individual structures of the peptides are well predicted, the assay captures the higher affinity binder in the bound state, and the other peptide in the unbound form with statistical significance. We test the application on six protein receptors for which we have experimental binding affinities to several peptides. We find that the assay is best suited for identifying medium to strong peptide binders that adopt stable secondary structures upon binding.

Deciphering the Folding Mechanism of Proteins G and L and Their Mutants.

Much of our understanding of folding mechanisms comes from interpretations of experimental ϕ and ψ value analysis, relating the differences in stability of the transition state ensemble (TSE) and folded state. We introduce a unified approach combining simulations and Bayesian inference to provide atomistic detail for the folding mechanism of proteins G and L and their mutants. Proteins G and L fold to similar topologies despite low sequence similarity, but differ in their folding pathways. A fast folding redesign of protein G, NuG2, switches folding pathways and folds through a similar pathway with protein L. A redesign of protein L also leads to faster folding, respecting the original folding pathway. Our Bayesian inference approach starts from the same prior on all systems and correctly identifies the folding mechanism for each of the four proteins, a success of the force field and sampling strategy. The approach is computationally efficient and correctly identifies the TSE and intermediate structures along the folding pathway in good agreement with experiments. We complement our findings by using two orthogonal approaches that differ in computational cost and interpretability. Adaptive sampling MD combined with the Markov state model provides a kinetic model that confirms the more complex folding mechanism of protein G and its mutant. Finally, a novel fragment decomposition approach using AlphaFold identifies preferences for secondary structure element combinations that follow the order of events observed in the folding pathways.

Deep Learning CT-based Quantitative Visualization Tool for Liver Volume Estimation: Defining Normal and Hepatomegaly.

Background Imaging assessment for hepatomegaly is not well defined and currently uses suboptimal, unidimensional measures. Liver volume provides a more direct measure for organ enlargement. Purpose To determine organ volume and to establish thresholds for hepatomegaly with use of a validated deep learning artificial intelligence tool that automatically segments the liver. Materials and Methods In this retrospective study, liver volumes were successfully derived with use of a deep learning tool for asymptomatic outpatient adults who underwent multidetector CT for colorectal cancer screening (unenhanced) or renal donor evaluation (contrast-enhanced) at a single medical center between April 2004 and December 2016. The performance of the craniocaudal and maximal three-dimensional (3D) linear measures was assessed. The manual liver volume results were compared with the automated results in a subset of renal donors in which the entire liver was included at both precontrast and postcontrast CT. Unenhanced liver volumes were standardized to a postcontrast equivalent, reflecting a correction of 3.6%. Linear regression analysis was performed to assess the major patient-specific determinant or determinants of liver volume among age, sex, height, weight, and body surface area. Results A total of 3065 patients (mean age ± standard deviation, 54 years ± 12; 1639 women) underwent multidetector CT for colorectal screening (n = 1960) or renal donor evaluation (n = 1105). The mean standardized automated liver volume ± standard deviation was 1533 mL ± 375 and demonstrated a normal distribution. Patient weight was the major determinant of liver volume and demonstrated a linear relationship. From this result, a linear weight-based upper limit of normal hepatomegaly threshold volume was derived: hepatomegaly (mL) = 14.0 × (weight [kg]) + 979. A craniocaudal threshold of 19 cm was 71% sensitive (49 of 69 patients) and 86% specific (887 of 1030 patients) for hepatomegaly, and a maximal 3D linear threshold of 24 cm was 78% sensitive (54 of 69) and 66% specific (678 of 1030). In the subset of 189 patients, the median difference in hepatic volume between the deep learning tool and the semiautomated or manual method was 2.3% (38 mL). Conclusion A simple weight-based threshold for hepatomegaly derived by using a fully automated CT-based liver volume segmentation based on deep learning provided an objective and more accurate assessment of liver size than linear measures. © RSNA, 2021 Online supplemental material is available for this article. See also the editorial by Sosna in this issue.

3DBionotes COVID-19 edition.

SUMMARY: The web platform 3DBionotes-WS integrates multiple web services and an interactive web viewer to provide a unified environment in which biological annotations can be analyzed in their structural context. Since the COVID-19 outbreak, new structural data from many viral proteins have been provided at a very fast pace. This effort includes many cryogenic electron microscopy (cryo-EM) studies, together with more traditional ones (X-rays, NMR), using several modeling approaches and complemented with structural predictions. At the same time, a plethora of new genomics and interactomics information (including fragment screening and structure-based virtual screening efforts) have been made available from different servers. In this context, we have developed 3DBionotes-COVID-19 as an answer to: (i) the need to explore multiomics data in a unified context with a special focus on structural information and (ii) the drive to incorporate quality measurements, especially in the form of advanced validation metrics for cryo-EM. AVAILABILITY AND IMPLEMENTATION: https://3dbionotes.cnb.csic.es/ws/covid19. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.