The HADDOCK2.4 web server for integrative modeling of biomolecular complexes.

Interactions between macromolecules, such as proteins and nucleic acids, are essential for cellular functions. Experimental methods can fail to provide all the information required to fully model biomolecular complexes at atomic resolution, particularly for large and heterogeneous assemblies. Integrative computational approaches have, therefore, gained popularity, complementing traditional experimental methods in structural biology. Here, we introduce HADDOCK2.4, an integrative modeling platform, and its updated web interface ( https://wenmr.science.uu.nl/haddock2.4 ). The platform seamlessly integrates diverse experimental and theoretical data to generate high-quality models of macromolecular complexes. The user-friendly web server offers automated parameter settings, access to distributed computing resources, and pre- and post-processing steps that enhance the user experience. To present the web server's various interfaces and features, we demonstrate two different applications: (i) we predict the structure of an antibody-antigen complex by using NMR data for the antigen and knowledge of the hypervariable loops for the antibody, and (ii) we perform coarse-grained modeling of PRC1 with a nucleosome particle guided by mutagenesis and functional data. The described protocols require some basic familiarity with molecular modeling and the Linux command shell. This new version of our widely used HADDOCK web server allows structural biologists and non-experts to explore intricate macromolecular assemblies encompassing various molecule types.

Sickle Cell Disease in an Older Adult Population: A Retrospective Review of Health Care Resource Utilization.

Sickle cell disease (SCD) has a history of health inequity, as patients with SCD are primarily Black and often marginalized from the health care system. Although recent health care and treatment advancements have prolonged life expectancy, it may be insufficient to support the complex needs of the growing population of older adults with SCD. This retrospective study used a cohort (N = 812) of Medicare Advantage beneficiaries 45 years and older (ages: 45-54, 55-64, 65-74, 75-89) with SCD to identify associations of SCD-related complications and comorbidities with emergency department (ED) visits, potentially avoidable ED visits, all-cause hospitalization, and potentially avoidable hospitalizations, 2018-2020. The 75-89 age group had lower odds of an ED visit (OR 0.56; 95% CI 0.32-1.00), 65-74 age group had lower odds of an ED visit (OR 0.49; 95% CI 0.31-0.78) and hospitalization (OR 0.50; 95% CI 0.31-0.79), compared with the 45-54 age group. Acute chest syndrome was associated with increased odds of an ED visit (OR 2.02; 95% CI 1.10-3.71), avoidable ED visit (OR 1.87; 95% CI 1.14-3.06), and hospitalization (OR 3.61; 95% CI 2.06-6.31). Pain was associated with increased odds of an ED visit (OR 2.64; 95% CI 1.85-3.76), an avoidable ED visit (OR 3.08; 95% CI 1.90-4.98), hospitalization (OR 1.51; 95% CI 1.02-2.24), and avoidable hospitalization (OR 6.42; 95% CI 1.74-23.74). Older adults with SCD have been living with SCD for decades, often while managing pain crises and complications associated increased incidence of an ED visit and hospitalization. The characteristics and needs of this population must continue to be examined to increase preventative care and reduce costly emergent health care resource utilization.

La actividad física como reductora de riesgo cardiovascular en personas hipertensas

Hoy día la hipertensión arterial es una enfermedad que afecta aproximadamente a la tercera parte de la población adulta a nivel mundial. Esta patología, a su vez, es el primer factor de riesgo cardiovascular, pero también un factor de riesgo de enfermedad renal crónica y demencia. Las enfermedades cardiovasculares constituyen la primera causa de muerte a nivel mundial, regional, nacional y provincial, por lo que son de vital importancia las acciones encaminadas al manejo, control y reducción del riesgo a desarrollarlas. La práctica saludable de ejercicio físico es una herramienta económica y efectiva como coadyuvante del tratamiento de la hipertensión arterial y reductora de riesgo cardiovascular. Tanto los ejercicios aeróbicos como anaeróbicos tienen efectos positivos sobre las cifras de presión arterial, ayudan a controlar los niveles de colesterol en sangre, y son efectivos contra la dislipidemia e incluso contra la diabetes mellitus, patologías que elevan aún más el riesgo cardiovascular. La actividad física saludable también combate el sedentarismo y regula el peso corporal. Sin embargo, el estado de actividad física no se tiene en cuenta directamente a la hora de estratificar el riesgo cardiovascular en los predictores usados actualmente en el país, que son los propuestos por la Organización Panamericana de la Salud. De ahí que este trabajo tenga como objetivo fundamentar el papel de la práctica de actividad física como reductora de riesgo cardiovascular en personas hipertensas.

Today, arterial hypertension is a disease that affects almost one third of the adult population worldwide. This disease, in turn, is the first cardiovascular risk factor, but also a risk factor for chronic renal disease and dementia. Cardiovascular diseases are the leading cause of dead at the global, regional, national and provincial levels, so actions aimed at managing, controlling and reducing the risk of developing them are of vital importance. The healthy practice of physical exercise is an effective and economic tool as an adjuvant to the treatment of arterial hypertension and reductor of cardiovascular risk. Both aerobic and anaerobic exercises have positive effects on blood pressure levels, help control blood cholesterol levels and are effective against dyslipidemia and even against diabetes mellitus, pathologies that further increase cardiovascular risk. Healthy physical activity also fights sedentary lifestyle and regulates body weight. However, the physical activity status is not directly taken into account when stratifying cardiovascular risk in the predictors currently used in the country that are those proposed by the Pan American Health Organization. That is why this work aims to substantiate the role of the practice of physical activity as cardiovascular risk reductor in hypertensive persons.

Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment.

We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody-antigen complexes, and 7 large assemblies. On average ~70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups and by 15 CAPRI scorer groups were evaluated using the CAPRI model quality measures and the DockQ score consolidating these measures. The prediction performance was quantified by a weighted score based on the number of models of acceptable quality or higher submitted by each group among their five best models. Results show substantial progress achieved across a significant fraction of the 60+ participating groups. High-quality models were produced for about 40% of the targets compared to 8% two years earlier. This remarkable improvement is due to the wide use of the AlphaFold2 and AlphaFold2-Multimer software and the confidence metrics they provide. Notably, expanded sampling of candidate solutions by manipulating these deep learning inference engines, enriching multiple sequence alignments, or integration of advanced modeling tools, enabled top performing groups to exceed the performance of a standard AlphaFold2-Multimer version used as a yard stick. This notwithstanding, performance remained poor for complexes with antibodies and nanobodies, where evolutionary relationships between the binding partners are lacking, and for complexes featuring conformational flexibility, clearly indicating that the prediction of protein complexes remains a challenging problem.

Rational Prediction of PROTAC-Compatible Protein-Protein Interfaces by Molecular Docking.

Proteolysis targeting chimeras (PROTACs) are heterobifunctional ligands that mediate the interaction between a protein target and an E3 ligase, resulting in a ternary complex, whose interaction with the ubiquitination machinery leads to target degradation. This technology is emerging as an exciting new avenue for therapeutic development, with several PROTACs currently undergoing clinical trials targeting cancer. Here, we describe a general and computationally efficient methodology combining restraint-based docking, energy-based rescoring, and a filter based on the minimal solvent-accessible surface distance to produce PROTAC-compatible PPIs suitable for when there is no a priori known PROTAC ligand. In a benchmark employing a manually curated data set of 13 ternary complex crystals, we achieved an accuracy of 92% when starting from bound structures and 77% when starting from unbound structures, respectively. Our method only requires that the ligand-bound structures of the monomeric forms of the E3 ligase and target proteins be given to run, making it general, accurate, and highly efficient, with the ability to impact early-stage PROTAC-based drug design campaigns where no structural information about the ternary complex structure is available.

Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study.

Reliably scoring and ranking candidate models of protein complexes and assigning their oligomeric state from the structure of the crystal lattice represent outstanding challenges. A community-wide effort was launched to tackle these challenges. The latest resources on protein complexes and interfaces were exploited to derive a benchmark dataset consisting of 1677 homodimer protein crystal structures, including a balanced mix of physiological and non-physiological complexes. The non-physiological complexes in the benchmark were selected to bury a similar or larger interface area than their physiological counterparts, making it more difficult for scoring functions to differentiate between them. Next, 252 functions for scoring protein-protein interfaces previously developed by 13 groups were collected and evaluated for their ability to discriminate between physiological and non-physiological complexes. A simple consensus score generated using the best performing score of each of the 13 groups, and a cross-validated Random Forest (RF) classifier were created. Both approaches showed excellent performance, with an area under the Receiver Operating Characteristic (ROC) curve of 0.93 and 0.94, respectively, outperforming individual scores developed by different groups. Additionally, AlphaFold2 engines recalled the physiological dimers with significantly higher accuracy than the non-physiological set, lending support to the reliability of our benchmark dataset annotations. Optimizing the combined power of interface scoring functions and evaluating it on challenging benchmark datasets appears to be a promising strategy.

The LightDock Server: Artificial Intelligence-powered modeling of macromolecular interactions.

Computational docking is an instrumental method of the structural biology toolbox. Specifically, integrative modeling software, such as LightDock, arise as complementary and synergetic methods to experimental structural biology techniques. Ubiquitousness and accessibility are fundamental features to promote ease of use and to improve user experience. With this goal in mind, we have developed the LightDock Server, a web server for the integrative modeling of macromolecular interactions, along with several dedicated usage modes. The server builds upon the LightDock macromolecular docking framework, which has proved useful for modeling medium-to-high flexible complexes, antibody-antigen interactions, or membrane-associated protein assemblies. We believe that this free-to-use resource will be a valuable addition to the structural biology community and can be accessed online at: https://server.lightdock.org/.

The influence of accessory dwelling unit (ADU) policy on the contributing factors to ADU development: an assessment of the city of Los Angeles.

Since the accessory dwelling unit (ADU) has emerged as a policy alternative to increase housing stock and provide affordable options for areas impacted by housing shortages, many local governments recently adopted ADU policies that promote the construction of ADUs. Taking the City of Los Angeles as the study area, this paper examines how the city's ADU ordinance impacts the relationship of the characteristics of the properties and neighborhoods with ADU development by constructing multilevel logistic regression models. The outputs of the models suggest that the ordinance contributes to diversifying the types and locations of the properties and neighborhoods where ADUs are built. The influence of the property characteristics associated with ADU development before the implementation of the ordinance significantly diminished after the ordinance. The outputs also indicate that the ordinance probably attracted ADU developments in the areas with higher accessibility to bus transit. These findings will help planners take appropriate actions and policies that support ADU developments.

pyDockDNA: A new web server for energy-based protein-DNA docking and scoring.

Proteins and nucleic acids are essential biological macromolecules for cell life. Indeed, interactions between proteins and DNA regulate many biological processes such as protein synthesis, signal transduction, DNA storage, or DNA replication and repair. Despite their importance, less than 4% of total structures deposited in the Protein Data Bank (PDB) correspond to protein-DNA complexes, and very few computational methods are available to model their structure. We present here the pyDockDNA web server, which can successfully model a protein-DNA complex with a reasonable predictive success rate (as benchmarked on a standard dataset of protein-DNA complex structures, where DNA is in B-DNA conformation). The server implements the pyDockDNA program, as a module of pyDock suite, thus including third-party programs, modules, and previously developed tools, as well as new modules and parameters to handle the DNA properly. The user is asked to enter Protein Data Bank files for protein and DNA input structures (or suitable models) and select the chains to be docked. The server calculations are mainly divided into three steps: sampling by FTDOCK, scoring with new energy-based parameters and the possibility of applying external restraints. The user can select different options for these steps. The final output screen shows a 3D representation of the top 10 models and a table sorting the model according to the scoring function selected previously. All these output files can be downloaded, including the top 100 models predicted by pyDockDNA. The server can be freely accessed for academic use (https://model3dbio.csic.es/pydockdna).

Clinical Outcomes for Open Hip Abductor Repair Using Tenodesis and Bone Trough Repair Techniques.

BACKGROUND: Hip abductor complex tears remain an injury without a clear consensus on management. Surgical treatment has been recommended after unsuccessful nonoperative management. This study evaluates both tenodesis and bone trough techniques, with treatment choices guided by previously described tear classification. METHODS: This is a retrospective cohort study of 45 hips in 44 patients who underwent surgical treatment for symptomatic, chronic hip abductor tear unresponsive to nonoperative treatment. Demographics and preoperative and postoperative values (including visual analog scale pain scores, gait assessment, and muscle strength) were evaluated. Type I tears were treated using tendon tenodesis. Type II tears were treated through a bone trough repair. RESULTS: Forty-five hips (44 patients) were operated on with a minimum of 6-month follow-up. There were 27 type I and 18 type II tears. Eighty-seven percent of patients were female. Twenty-eight percent of type II patients (5/18) had a preexisting arthroplasty in place. Significant improvements in pain (P < .001), gait (P < .001), and muscle strength (P < .001) were achieved in both the tear types. Type I repairs showed superior results to type II repairs. However, both showed significant improvements. Postoperative magnetic resonance imaging at 6 months showed healed tenodesis in 81% (17/21) of type I tears and 50% (5/10) of type II tears. CONCLUSION: Our study shows improvement in pain and function after surgical repair of hip abductor tendon injuries in both simple and complex tears. This improvement is seen even during ongoing surgical site healing. Magnetic resonance imaging findings may remain abnormal for more than 1 year after surgery and do not clearly denote repair failure.

Towards design of drugs and delivery systems with the Martini coarse-grained model.

Coarse-grained (CG) modelling with the Martini force field has come of age. By combining a variety of bead types and sizes with a new mapping approach, the newest version of the model is able to accurately simulate large biomolecular complexes at millisecond timescales. In this perspective, we discuss possible applications of the Martini 3 model in drug discovery and development pipelines and highlight areas for future development. Owing to its high simulation efficiency and extended chemical space, Martini 3 has great potential in the area of drug design and delivery. However, several aspects of the model should be improved before Martini 3 CG simulations can be routinely employed in academic and industrial settings. These include the development of automatic parameterisation protocols for a variety of molecule types, the improvement of backmapping procedures, the description of protein flexibility and the development of methodologies enabling efficient sampling. We illustrate our view with examples on key areas where Martini could give important contributions such as drugs targeting membrane proteins, cryptic pockets and protein-protein interactions and the development of soft drug delivery systems.

UDock2: interactive real-time multi-body protein-protein docking software.

MOTIVATION: Protein-protein docking aims at predicting the geometry of protein interactions to gain insights into the mechanisms underlying these processes and develop new strategies for drug discovery. Interactive and user-oriented manipulation tools can support this task complementary to automated software. RESULTS: This article presents an interactive multi-body protein-protein docking software, UDock2, designed for research but also usable for teaching and popularization of science purposes due to its high usability. In UDock2, the users tackle the conformational space of protein interfaces using an intuitive real-time docking procedure with on-the-fly scoring. UDock2 integrates traditional computer graphics methods to facilitate the visualization and to provide better insight into protein surfaces, interfaces, and properties. AVAILABILITY AND IMPLEMENTATION: UDock2 is open-source, cross-platform (Windows and Linux), and available at http://udock.fr. The code can be accessed at https://gitlab.com/Udock/Udock2.

Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment.

We present the results for CAPRI Round 50, the fourth joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of twelve targets, including six dimers, three trimers, and three higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly related templates were found for the individual subunits. Twenty-five CAPRI groups including eight automatic servers submitted ~1250 models per target. Twenty groups including six servers participated in the CAPRI scoring challenge submitted ~190 models per target. The accuracy of the predicted models was evaluated using the classical CAPRI criteria. The prediction performance was measured by a weighted scoring scheme that takes into account the number of models of acceptable quality or higher submitted by each group as part of their five top-ranking models. Compared to the previous CASP-CAPRI challenge, top performing groups submitted such models for a larger fraction (70-75%) of the targets in this Round, but fewer of these models were of high accuracy. Scorer groups achieved stronger performance with more groups submitting correct models for 70-80% of the targets or achieving high accuracy predictions. Servers performed less well in general, except for the MDOCKPP and LZERD servers, who performed on par with human groups. In addition to these results, major advances in methodology are discussed, providing an informative overview of where the prediction of protein assemblies currently stands.

Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem.

Structural biology aims at characterizing the structural and dynamic properties of biological macromolecules at atomic details. Gaining insight into three dimensional structures of biomolecules and their interactions is critical for understanding the vast majority of cellular processes, with direct applications in health and food sciences. Since 2010, the WeNMR project (www.wenmr.eu) has implemented numerous web-based services to facilitate the use of advanced computational tools by researchers in the field, using the high throughput computing infrastructure provided by EGI. These services have been further developed in subsequent initiatives under H2020 projects and are now operating as Thematic Services in the European Open Science Cloud portal (www.eosc-portal.eu), sending >12 millions of jobs and using around 4,000 CPU-years per year. Here we review 10 years of successful e-infrastructure solutions serving a large worldwide community of over 23,000 users to date, providing them with user-friendly, web-based solutions that run complex workflows in structural biology. The current set of active WeNMR portals are described, together with the complex backend machinery that allows distributed computing resources to be harvested efficiently.

Contemporary Imaging of the Surgically Placed Hepatic Arterial Infusion Chemotherapy Pump.

Hepatic arterial infusion (HAI) of chemotherapy is a locoregional treatment strategy for hepatic malignancy involving placement of a surgically implanted pump or percutaneous port-catheter device into a branch of the hepatic artery. HAI has been used for metastatic colorectal cancer for decades but has recently attracted new attention because of its potential impact on survival, when combined with systemic therapy, in patients presenting with unresectable hepatic disease. Although various HAI device-related complications have been described, little attention has been given to their appearance on imaging. Radiologists are uniquely positioned to identify these complications given that patients receiving HAI therapy typically undergo frequent imaging and may have complications that are delayed or clinically unsuspected. Therefore, this article reviews the multimodality imaging considerations of surgically implanted HAI devices. The role of imaging in routine perioperative assessment, including the normal postoperative appearance of the device, is described. The imaging findings of potential complications, including pump pocket complications, catheter or arterial complications, and toxic or ischemic complications, are presented, with a focus on CT. Familiarity with the device and its complications will aid radiologists in playing an important role in the treatment of patients undergoing HAI therapy.

Phenoxy Radical Reactivity of Nucleic Acids: Practical Implications for Biotinylation.

Recent advances in peroxidase-mediated biotin tyramide (BT) signal amplification technology have resulted in high-resolution and subcellular compartment-specific mapping of protein and RNA localization. Horseradish peroxidase (HRP) in the presence of H2 O2 is known to activate phenolic compounds for phenoxy radical reaction with nucleic acids, where biotinylation by BT is a practical example. BT reactivity with RNA and DNA is not understood in detail. We report that BT phenoxy radicals react in a sequence-independent manner with guanosine bases in RNA. In contrast, DNA reactivity with BT cannot be detected by our methods under the same conditions. Remarkably, we show that fluorescein conjugates DNA rapidly and selectively reacts with BT phenoxy radicals, allowing convenient and practical biotinylation of DNA on fluorescein with retention of fluorescence.

PDB-tools web: A user-friendly interface for the manipulation of PDB files.

The Protein Data Bank (PDB) file format remains a popular format used and supported by many software to represent coordinates of macromolecular structures. It however suffers from drawbacks such as error-prone manual editing. Because of that, various software toolkits have been developed to facilitate its editing and manipulation, but, to date, there is no online tool available for this purpose. Here we present PDB-Tools Web, a flexible online service for manipulating PDB files. It offers a rich and user-friendly graphical user interface that allows users to mix-and-match more than 40 individual tools from the pdb-tools suite. Those can be combined in a few clicks to perform complex pipelines, which can be saved and uploaded. The resulting processed PDB files can be visualized online and downloaded. The web server is freely available at https://wenmr.science.uu.nl/pdbtools.

Integrative modeling of membrane-associated protein assemblies.

Membrane proteins are among the most challenging systems to study with experimental structural biology techniques. The increased number of deposited structures of membrane proteins has opened the route to modeling their complexes by methods such as docking. Here, we present an integrative computational protocol for the modeling of membrane-associated protein assemblies. The information encoded by the membrane is represented by artificial beads, which allow targeting of the docking toward the binding-competent regions. It combines efficient, artificial intelligence-based rigid-body docking by LightDock with a flexible final refinement with HADDOCK to remove potential clashes at the interface. We demonstrate the performance of this protocol on eighteen membrane-associated complexes, whose interface lies between the membrane and either the cytosolic or periplasmic regions. In addition, we provide a comparison to another state-of-the-art docking software, ZDOCK. This protocol should shed light on the still dark fraction of the interactome consisting of membrane proteins.