Exploring alternatives for securing anatomical structures in capturing digital images: A comparative analysis.

Teaching veterinary anatomy using digital platforms requires improved image quality, which may influence the fixation process. This study aimed to compare four embalming solutions for high-colour-quality images of different tissues compared to the original image. Four equine left pelvic limbs were cut into metameres and divided equally for application of 10% formaldehyde, 96% glycerine, 33% hypersaturated NaCl solution and modified Larssen solution, respectively, which was maintained for 3 days. After drying for 3 days at room temperature, photographs were obtained at time 0 (T0), without any fixation process (original colour); time 1 (T1), immediately after removal from the solutions; and every 24 h for 3 days (T2-T4). The image colour quality was investigated by digitally evaluating the cortical bone, tendon and bone marrow using histograms and CIEDE2000 as well as by 10 specialists in an online survey. CIEDE2000 and histograms revealed that all fixation solutions changed the original tissue colour at all the time points (p < 0.0001). According to the specialists, the 33% saline solution produced the best results compared to the original one. The modified Larssen solution demonstrated better results for the tendon, marrow and cortical bone at T3 (p = 0.0015). Considering the colour of digital images, the modified Larssen solution provided the best results; however, the visual evaluation by the specialists revealed the 33% saline solution as the best.

Utilizing intramammary Melaleuca alternifolia as an organic internal sealant for dry-off therapy in Murrah buffaloes.

The effects of intramammary dry cow therapy based on the administration of 5% Melaleuca alternifolia tea tree essential oil (TTO) as an internal teat sealant to Murrah cows were evaluated. A longitudinal prospective and retrospective negative control study was performed using 12 buffaloes from a total of 20 Murrah buffaloes on an organic farm, with the cow used as a control for herself. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) for treatments with pure oil (TTO) and medication containing 5% TTO (O5) were determined. The buffaloes were clinically examined, and the teats were evaluated using thermography and ultrasound. Udder health was monitored during the first 100 days in milk (DIM) using milk somatic cell count (SCC) and California mastitis test (CMT). Laboratory tests against standard strains Staphylococcus aureus ATCC®25,923™, Escherichia coli ATCC®25,922™, and wild bacterial strains showed maximum MIC values of 50 µL/mL for the TTO and O5 treatments. One wild-type S. aureus strain showed no MBC. No adverse effects were observed after the intramammary application of TTO. The CMT and SCC values were similar (P > 0.05) for all observations. The medication containing 5% TTO was effective in vitro and compatible with the intramammary tissue in vivo of Murrah buffaloes. TTO was safe, not inducing inflammatory processes or other modifications of the teat detectable by thermography or ultrasound. It was able to protect buffaloes during the dry period under field conditions, demonstrating potential use as a teat sealant for organic farms.

A remote, fully oriented personalized program of physical exercise for women in follow-up after breast cancer treatment improves body composition and physical fitness.

This study aimed to evaluate the efficacy of an individualized remote exercise program on the improvement of body composition and physical fitness of a heterogeneous group of patients who completed breast cancer treatment. This prospective study included 107 women aged 18 to 60, shortly after curative treatment for localized breast cancer, at the Erasto Gaertner Cancer Hospital (HEG) in Curitiba, PR, Brazil. Body composition, maximal oxygen consumption, and muscle resistance were evaluated after nine months of intervention while considering adherence to the program, level of physical activity, presence of binge eating disorder, tumor classification, and treatment type. Seventy-eight women (72.8%) adhered to the training program. Adherent participants showed significant changes in body mass ([-4.3 â€‹± â€‹3.6] kg; p â€‹< â€‹0.000 1), body mass index ([-1.6 â€‹± â€‹1.5] kg·m-2; p â€‹< â€‹0.000 1), body fat (-3.4% â€‹± â€‹3.1%; p â€‹< â€‹0.000 1), maximal oxygen consumption ([7.5 â€‹± â€‹2.0] ml·kg-1·min-1); p â€‹< â€‹0.000 1), and abdominal resistance ([11.2 â€‹± â€‹2.8] reps; p â€‹< â€‹0.000 1). In contrast, these variables did not change significantly in the non-adherent group. Among the adherent participants, those subclassified in the severe binge group showed a more noticeable reduction in body mass, body mass index, and body fat (p â€‹< â€‹0.05) than those in the non-binge group. Individualized remotely-guided physical exercise programs can improve the body composition and physical fitness of women undergoing post-breast cancer surveillance, regardless of pathological history or treatment.

Nontrivial effect of dephasing: Enhancement of rectification of spin current in graded XX chains.

In order to reveal mechanisms to control and manipulate spin currents, we perform a detailed investigation of the dephasing effects in the open XX model with a Lindblad dynamics involving global dissipators and thermal baths. Specifically, we consider dephasing noise modeled by current-preserving Lindblad dissipators acting on graded versions of these spin systems, that is, systems in which the magnetic field and/or the spin interaction are growing (decreasing) along the chain. In our analysis, we study the nonequilibrium steady state via the covariance matrix using the Jordan-Wigner approach to compute the spin currents. We find that the interplay between dephasing and graded systems gives rise to a nontrivial behavior: When we have homogeneous magnetic field and graded interactions we have rectification enhancement mechanisms, and when we have fully graded systems we can control the spin current in order to keep the direction of the particle and/or spin flow even with inverted baths. We describe our result in detailed numerical analysis and we see that rectification in this simple model indicates that the phenomenon may generally occur in quantum spin systems.

Ligand binding remodels protein side-chain conformational heterogeneity.

While protein conformational heterogeneity plays an important role in many aspects of biological function, including ligand binding, its impact has been difficult to quantify. Macromolecular X-ray diffraction is commonly interpreted with a static structure, but it can provide information on both the anharmonic and harmonic contributions to conformational heterogeneity. Here, through multiconformer modeling of time- and space-averaged electron density, we measure conformational heterogeneity of 743 stringently matched pairs of crystallographic datasets that reflect unbound/apo and ligand-bound/holo states. When comparing the conformational heterogeneity of side chains, we observe that when binding site residues become more rigid upon ligand binding, distant residues tend to become more flexible, especially in non-solvent-exposed regions. Among ligand properties, we observe increased protein flexibility as the number of hydrogen bonds decreases and relative hydrophobicity increases. Across a series of 13 inhibitor-bound structures of CDK2, we find that conformational heterogeneity is correlated with inhibitor features and identify how conformational changes propagate differences in conformational heterogeneity away from the binding site. Collectively, our findings agree with models emerging from nuclear magnetic resonance studies suggesting that residual side-chain entropy can modulate affinity and point to the need to integrate both static conformational changes and conformational heterogeneity in models of ligand binding.

Proteins are the workhorses of our cells. They are large molecules that 'fold' into specific, often highly complex, three-dimensional configurations. These structures are not static, but rather dynamic and flexible. In other words, proteins can shift between different three-dimensional shapes to perform their tasks within the cell. To perform their roles, many proteins have to bind to small molecule ligands. Many ligands are drugs, which means that their effectiveness depends on their ability to bind to and impact the proteins involved in the disease they are treating. When a ligand binds to a protein, it can reshape the protein. For example, certain conformations of the protein, which were difficult for the protein to be in on its own, may become more stable when the ligand binds. Additionally, upon ligand binding, some parts of the protein may move relative to each other. Previous studies have shown that these movements can affect the interaction between ligand and protein. However, these studies only examined a small number of proteins. Therefore, Wankowicz et al. set out to determine, in greater detail, what happens to protein flexibility upon ligand binding. First, a pipeline was created to model alternative configurations of the protein both with and without ligands attached. These models measured flexibility within protein structures. The models revealed that when ligands bind to proteins, the flexibility of different regions of the protein changes ­ and does so in a consistent way. Proteins that become more rigid in the region interacting with their ligands become less rigid in other, distant regions, and vice versa. In other words, the rest of the protein is able to compensate for any changes in flexibility caused by ligand binding, which may contribute to how well a ligand binds to a protein. This study demonstrates the ability of ligands to affect the entire structure of the proteins they bind to, and therefore sheds new light on the role of proteins' innate conformational flexibility during this process. These results will contribute to our understanding of how the ligands and proteins involved in different cellular processes interact with each other ­ and, potentially, how these interactions can be manipulated.

Induced Stress and Tactile Stimulation Applied to Primiparous does and their Consequences on Maternal Behavior, Human-Animal Relationships, and Future Offspring's Sexual Disorders.

The aim of this study was to investigate whether tactile stimulation in rabbits during the gestation phase improve the maternal behavior and human-animal relationships as well as the effects on reproductive behavior of male kits when reached maturity compared to induced stress. A total of 33 primiparous New Zealand does were selected after pregnancy confirmation and allocated in a randomized complete block design. The treatments applied were as follows: (C) animals not stimulated during the experimental period; (TS) animals that received tactile stimulation; and (SS) does which were immobilized. The nest building behavior as well as the weight, sexual behavior, mortality, and semen analysis of the offspring was recorded. In addition, the novel object, flight distance, social isolation, and human-approach tests were conducted. Under the conditions of the present trial, TS animals showed more trust in the unfamiliar observer when compared to the other two treatments. The treatments applied to the females (TS and SS) were sufficient to confirm that the control group presented better values for the number of stillbirths and the proportion of deaths in the first week. Finally, the handling of does reduce the males' ejaculation and sperm presence but not inhibited sexual behavior or impaired semen quality. It is possible to conclude that TS did not impair does welfare or maternal behavior and it improved the human-animal relationship, however there was a negative impact on the litter. More studies that directly assess impact on the future reproductive capacity of the offspring are necessary.

Effect of education and multimorbidity on mortality among older adults: findings from the health, well-being and ageing cohort study (SABE).

OBJECTIVES: This study assessed the moderating role of education on the relationship between multimorbidity and mortality among older adults in Brazil. STUDY DESIGN: This was a cohort study. METHODS: This study used data from 1768 participants of the Health, Well-Being and Ageing Cohort Study (SABE) who were assessed between 2006 and 2015. The Cox Proportional Risks Model was used to evaluate the association between multimorbidity (two or more chronic diseases) and mortality. An interaction term between education and multimorbidity was included to test the moderating role of education in this association. RESULTS: The average follow-up time was 4.5 years, with a total of 589 deaths in the period. Multimorbidity increased the risk of mortality (hazard ratio [HR] 1.55, 95% confidence interval [CI] 1.27-1.91), and this association was not moderated by education (HR 1.06, 95% CI 1.00-1.13; P value = 0.07). CONCLUSIONS: The impact of education and multimorbidity on mortality emphasises the need for an integrated approach directed towards the social determinants of health to prevent multimorbidity and its burden among older adults.

qFit 3: Protein and ligand multiconformer modeling for X-ray crystallographic and single-particle cryo-EM density maps.

New X-ray crystallography and cryo-electron microscopy (cryo-EM) approaches yield vast amounts of structural data from dynamic proteins and their complexes. Modeling the full conformational ensemble can provide important biological insights, but identifying and modeling an internally consistent set of alternate conformations remains a formidable challenge. qFit efficiently automates this process by generating a parsimonious multiconformer model. We refactored qFit from a distributed application into software that runs efficiently on a small server, desktop, or laptop. We describe the new qFit 3 software and provide some examples. qFit 3 is open-source under the MIT license, and is available at https://github.com/ExcitedStates/qfit-3.0.

Beyond the Lindblad master equation: Heat, work, and energy currents in boundary-driven spin chains.

We consider accurate investigation of the energy current and its components, heat and work, in some boundary-driven quantum spin systems. The expressions for the currents, as well as the associated Lindblad master equation, are obtained via a repeated interaction scheme. We consider small systems in order to analytically compute the steady distribution to study the current in the steady state. Asymmetrical XXZ and quantum Ising models are detailed analyzed. For the XXZ chain we present cases in which different compositions of heat and work currents, obtained via the repeated interaction protocol, lead to the same energy current, which may be obtained via the Lindblad master equation. For the quantum Ising chain, we describe a case of zero energy current and novanishing heat and work currents. Our findings make clear that to talk about heat in these boundary-driven spin quantum systems we must go beyond an investigation involving only the Lindblad master equation.

Prevalence of Juvenile Osteochondral Conditions in Yearling Thoroughbred Racehorses in Southern Brazil.

This study aimed to investigate the prevalence of juvenile osteochondral conditions (JOCCs) in yearling Thoroughbred (TB) racehorses in Southern Brazil, as well as to examine the same animals studied as weanlings by Bastos et al. (2017) and compare the radiographic findings for the two ages. Radiographs of 76 male and female TB yearlings from Paraná State, Southern Brazil, were investigated. The proximal interphalangeal, metacarpophalangeal/metatarsophalangeal (MC/MT), tarsal, and femorotibial (FT) joints were evaluated using 24 radiographic projections. The evaluation consisted of a severity index (rated as 0, 1, 2, 4, or 8), the sum of which resulted in an osteoarticular status (OAS) of good, intermediate, or poor for each animal. Radiographs of 92% of the investigated animals presented at least one finding consistent with JOCCs. The most affected region was the tarsal joint (72.9%), followed by the FT (50%), MT (25%), and MC (23%) joints. Thirty-three (43.4%) horses presented a decline in their OAS, whereas nine (11.8%) presented an improvement from the weanling to yearling age. The radiographic findings suggest that JOCCs are frequent in TB yearlings, but the meaning and relevance of these radiographic findings require further study.

Infrared Thermography Applied to Monitoring Musculoskeletal Adaptation to Training in Thoroughbred Race Horses.

Infrared thermography has been used to help in diagnosing lameness. It is hypothesized that, if used in a routine basis, it could help in understanding musculoskeletal modifications during race training. This study aimed to evaluate thermal variation in the musculoskeletal regions of young Thoroughbred (TB) horses during their initial months of race training. Thermographic examinations were performed once every 2 weeks on 16 (10 male, 6 female) two-year-old TB racehorses, from arrival to the racetrack in June 2016, until January 2017, for a total of 16 evaluations. Thermographic imaging was performed using the appropriate protocol. Temperature (°C) was measured at the dorsal and palmar/plantar aspects of specific regions of interest (fetlock, metacarpal, metatarsal, carpal, tarsal, thoracolumbar, sacroiliac spine, and both hips). Initially, we found a thermal balance and all regions demonstrated a positive correlation with one another. However, a significant difference was noted between the left and right sides as training progressed. Four horses were withdrawn from the study after 50% of evaluations because of metacarpal conditions associated with training. Thermographic examination revealed changes before the clinical manifestation of these conditions. In conclusion, this study demonstrated that infrared thermography is an image technique that can facilitate understanding of musculoskeletal system modifications to race training and should be further investigated as a predictive tool to anticipate the occurrence of lesions.

Heat rectification on the XX chain.

In order to better understand the minimal ingredients for thermal rectification, we perform a detailed investigation of a simple spin chain, namely, the open XX model with a Lindblad dynamics involving global dissipators. We use a Jordan-Wigner transformation to derive a mathematical formalism to compute the heat currents and other properties of the steady state. We have rigorous results to prove the occurrence of thermal rectification even for slightly asymmetrical chains. Interestingly, we describe cases where the rectification does not decay to zero as we increase the system size, that is, the rectification remains finite in the thermodynamic limit. We also describe some numerical results for more asymmetrical chains. The presence of thermal rectification in this simple model indicates that the phenomenon is of general occurrence in quantum spin systems.

The evolution of contact prediction: evidence that contact selection in statistical contact prediction is changing.

MOTIVATION: Over the last few years, the field of protein structure prediction has been transformed by increasingly accurate contact prediction software. These methods are based on the detection of coevolutionary relationships between residues from multiple sequence alignments (MSAs). However, despite speculation, there is little evidence of a link between contact prediction and the physico-chemical interactions which drive amino-acid coevolution. Furthermore, existing protocols predict only a fraction of all protein contacts and it is not clear why some contacts are favoured over others. Using a dataset of 863 protein domains, we assessed the physico-chemical interactions of contacts predicted by CCMpred, MetaPSICOV and DNCON2, as examples of direct coupling analysis, meta-prediction and deep learning. RESULTS: We considered correctly predicted contacts and compared their properties against the protein contacts that were not predicted. Predicted contacts tend to form more bonds than non-predicted contacts, which suggests these contacts may be more important than contacts that were not predicted. Comparing the contacts predicted by each method, we found that metaPSICOV and DNCON2 favour accuracy, whereas CCMPred detects contacts with more bonds. This suggests that the push for higher accuracy may lead to a loss of physico-chemically important contacts. These results underscore the connection between protein physico-chemistry and the coevolutionary couplings that can be derived from MSAs. This relationship is likely to be relevant to protein structure prediction and functional analysis of protein structure and may be key to understanding their utility for different problems in structural biology. AVAILABILITY AND IMPLEMENTATION: We use publicly available databases. Our code is available for download at https://opig.stats.ox.ac.uk/. SUPPLEMENTARY INFORMATION: Supplementary information is available at Bioinformatics online.

Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis.

How changes in enzyme structure and dynamics facilitate passage along the reaction coordinate is a fundamental unanswered question. Here, we use time-resolved mix-and-inject serial crystallography (MISC) at an X-ray free electron laser (XFEL), ambient-temperature X-ray crystallography, computer simulations, and enzyme kinetics to characterize how covalent catalysis modulates isocyanide hydratase (ICH) conformational dynamics throughout its catalytic cycle. We visualize this previously hypothetical reaction mechanism, directly observing formation of a thioimidate covalent intermediate in ICH microcrystals during catalysis. ICH exhibits a concerted helical displacement upon active-site cysteine modification that is gated by changes in hydrogen bond strength between the cysteine thiolate and the backbone amide of the highly strained Ile152 residue. These catalysis-activated motions permit water entry into the ICH active site for intermediate hydrolysis. Mutations at a Gly residue (Gly150) that modulate helical mobility reduce ICH catalytic turnover and alter its pre-steady-state kinetic behavior, establishing that helical mobility is important for ICH catalytic efficiency. These results demonstrate that MISC can capture otherwise elusive aspects of enzyme mechanism and dynamics in microcrystalline samples, resolving long-standing questions about the connection between nonequilibrium protein motions and enzyme catalysis.

RFQAmodel: Random Forest Quality Assessment to identify a predicted protein structure in the correct fold.

While template-free protein structure prediction protocols now produce good quality models for many targets, modelling failure remains common. For these methods to be useful it is important that users can both choose the best model from the hundreds to thousands of models that are commonly generated for a target, and determine whether this model is likely to be correct. We have developed Random Forest Quality Assessment (RFQAmodel), which assesses whether models produced by a protein structure prediction pipeline have the correct fold. RFQAmodel uses a combination of existing quality assessment scores with two predicted contact map alignment scores. These alignment scores are able to identify correct models for targets that are not otherwise captured. Our classifier was trained on a large set of protein domains that are structurally diverse and evenly balanced in terms of protein features known to have an effect on modelling success, and then tested on a second set of 244 protein domains with a similar spread of properties. When models for each target in this second set were ranked according to the RFQAmodel score, the highest-ranking model had a high-confidence RFQAmodel score for 67 modelling targets, of which 52 had the correct fold. At the other end of the scale RFQAmodel correctly predicted that for 59 targets the highest-ranked model was incorrect. In comparisons to other methods we found that RFQAmodel is better able to identify correct models for targets where only a few of the models are correct. We found that RFQAmodel achieved a similar performance on the model sets for CASP12 and CASP13 free-modelling targets. Finally, by iteratively generating models and running RFQAmodel until a model is produced that is predicted to be correct with high confidence, we demonstrate how such a protocol can be used to focus computational efforts on difficult modelling targets. RFQAmodel and the accompanying data can be downloaded from http://opig.stats.ox.ac.uk/resources.

Pressuring of Acupoints as a Complement to the Diagnosis of Stifle Diseases in Horses.

Diseases of the stifle joint remain a challenge for veterinarians. The objective of this study was to achieve a valuable acupuncture suggestive diagnosis to be considered for stifle joint diseases in horses. Thirty-nine nonlame horses involved in different activities were assessed. Acupuncture was independently performed by two evaluators. Reactions of the animal when pressurizing the point suggestive of stifle disease (PSSD), Bladder-20 and/or Bladder-21, were considered as the inclusion criteria for inclusion in the stifle group (SG, n = 31), and the animals with no reactions were assigned to the control group (n = 8). Radiographic and ultrasonographic examinations were performed and evaluated by two independent professionals blinded to the group allocation. Thermographic examination of the PSSD and stifles was also performed, after acclimatization. The ultrasound scores and radiographic findings were higher in the SG than in the control group. Thermography evidenced increased temperature in the PSSD and stifles in the SG. The minimum acupuncture diagnostic criteria for stifle joint disease had a sensitivity of 87.5% and a specificity of 57.0%, and the addition of the acupoints Gallbladder-dorsal tuber coxae, Gallbladder-27, and Spleen-13 to the minimum diagnostic criteria improved sensitivity and specificity. In conclusion, assessing the reaction at the demonstrated acupoints can facilitate a diagnosis of a potential stifle lesion.

qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps.

Proteins and ligands sample a conformational ensemble that governs molecular recognition, activity, and dissociation. In structure-based drug design, access to this conformational ensemble is critical to understand the balance between entropy and enthalpy in lead optimization. However, ligand conformational heterogeneity is currently severely underreported in crystal structures in the Protein Data Bank, owing in part to a lack of automated and unbiased procedures to model an ensemble of protein-ligand states into X-ray data. Here, we designed a computational method, qFit-ligand, to automatically resolve conformationally averaged ligand heterogeneity in crystal structures, and applied it to a large set of protein receptor-ligand complexes. In an analysis of the cancer related BRD4 domain, we found that up to 29% of protein crystal structures bound with drug-like molecules present evidence of unmodeled, averaged, relatively isoenergetic conformations in ligand-receptor interactions. In many retrospective cases, these alternate conformations were adventitiously exploited to guide compound design, resulting in improved potency or selectivity. Combining qFit-ligand with high-throughput screening or multitemperature crystallography could therefore augment the structure-based drug design toolbox.

Patterns of copy number alterations in primary breast tumors of South African patients and their impact on functional cellular pathways.

Breast cancer is the most common and the leading cause of female mortality among South African (SA) women. Several non­biological and biological risk factors may be attributed to their observed high mortality rate; however, the molecular profiles associated with their breast tumors are poorly characterized. The present study examined the patterns of genome-wide copy number alterations (CNAs) and their potential impact on functional cellular pathways targeted by cancer driver genes in patients with breast cancer from the Western Cape region of SA. Array-comparative genomic hybridization analysis, performed in 28 cases of invasive breast cancer, revealed a mean number of 8.68±6.18 CNAs per case, affecting primarily the Xp22.3 and 6p21-p25 cytobands (57.14% of the cases), followed by 19p13.3-p13.11 (35.7%), 2p25.3-p24.3, 4p16.3-p15.3, 8q11.1-q24.3 and 16 p13.3-p11.2 (32.14%). Functional enrichment analysis of genes and microRNA targets mapped in these affected cytobands revealed critical cancer-associated pathways, including fatty acid biosynthesis and metabolism, extracellular matrix-receptor interaction, hippo and tumor protein p53 signaling pathways, which are regulated by known cancer genes, including CCND1, CDKN1A, MAPK1, MDM2, TP53 and SMAD2. An inverse correlation was observed among the number of CNAs and tumor size and grade; CNAs on the 4p and 6p cytobands were also inversely correlated with tumor grade. No association was observed in the number of CNAs and/or the affected cytobands and the different ethnic groups of the SA patients, indicating that their tumor genome is affected by CNAs, irrespectively of their genetic descent. Additional genomic tumor profiling in SA and other Sub-Saharan African patients with breast cancer is required to determine the associations of the CNAs observed with prognosis and clinical outcome.

Combining co-evolution and secondary structure prediction to improve fragment library generation.

Motivation: Recent advances in co-evolution techniques have made possible the accurate prediction of protein structures in the absence of a template. Here, we provide a general approach that further utilizes co-evolution constraints to generate better fragment libraries for fragment-based protein structure prediction. Results: We have compared five different fragment library generation programmes on three different datasets encompassing over 400 unique protein folds. We show that considering the secondary structure of the fragments when assembling these libraries provides a critical way to assess their usefulness to structure prediction. We then use co-evolution constraints to improve the fragment libraries by enriching them with fragments that satisfy constraints and discarding those that do not. These improved libraries have better precision and lead to consistently better modelling results. Availability and implementation: Data is available for download from: http://opig.stats.ox.ac.uk/resources. Flib-Coevo is available for download from: https://github.com/sauloho/Flib-Coevo. Supplementary information: Supplementary data are available at Bioinformatics online.

STCRDab: the structural T-cell receptor database.

The Structural T-cell Receptor Database (STCRDab; http://opig.stats.ox.ac.uk/webapps/stcrdab) is an online resource that automatically collects and curates TCR structural data from the Protein Data Bank. For each entry, the database provides annotations, such as the α/ß or γ/δ chain pairings, major histocompatibility complex details, and where available, antigen binding affinities. In addition, the orientation between the variable domains and the canonical forms of the complementarity-determining region loops are also provided. Users can select, view, and download individual or bulk sets of structures based on these criteria. Where available, STCRDab also finds antibody structures that are similar to TCRs, helping users explore the relationship between TCRs and antibodies.