PDB-Explorer: a web-based interactive map of the protein data bank in shape space

Background The RCSB Protein Data Bank (PDB) provides public access to experimentally determined 3D-structures of biological macromolecules (proteins, peptides and nucleic acids). While various tools are available to explore the PDB, options to access the global structural diversity of the entire PDB and to perceive relationships between PDB structures remain very limited. Methods A 136-dimensional atom pair 3D-fingerprint for proteins (3DP) counting categorized atom pairs at increasing through-space distances was designed to represent the molecular shape of PDB-entries. Nearest neighbor searches examples were reported exemplifying the ability of 3DP-similarity to identify closely related biomolecules from small peptides to enzyme and large multiprotein complexes such as virus particles. The principle component analysis was used to obtain the visualization of PDB in 3DP-space. Results The 3DP property space groups proteins and protein assemblies according to their 3D-shape similarity, yet shows exquisite ability to distinguish between closely related structures. An interactive website called PDB-Explorer is presented featuring a color-coded interactive map of PDB in 3DP-space. Each pixel of the map contains one or more PDB-entries which are directly visualized as ribbon diagrams when the pixel is selected. The PDB-Explorer website allows performing 3DP-nearest neighbor searches of any PDB-entry or of any structure uploaded as protein-type PDB file. All functionalities on the website are implemented in JavaScript in a platform-independent manner and draw data from a server that is updated daily with the latest PDB additions, ensuring complete and up-to-date coverage. The essentially instantaneous 3DP-similarity search with the PDB-Explorer provides results comparable to those of much slower 3D-alignment algorithms, and automatically clusters proteins from the same superfamilies in tight groups. Conclusion A chemical space classification of PDB based on molecular shape was obtained using a new atom-pair 3D-fingerprint for proteins and implemented in a web-based database exploration tool comprising an interactive color-coded map of the PDB chemical space and a nearest neighbor search tool. The PDB-Explorer website is freely available at www.​cheminfo.​org/​pdbexplorer and represents an unprecedented opportunity to interactively visualize and explore the structural diversity of the PDB.

Evaluation of a web-based application versus conventional instruction in the undergraduate curriculum of fixed prosthodontics

The present study aims to investigate the implications of web-based delivery of identical learning content for time efficiency and students' performance, as compared to conventional textbook resources.

The InterHerz project--a web-based psychological treatment for cardiac patients with depression: study protocol of a randomized controlled trial

Patients with heart disease often suffer from difficulties in psychological adaptation during cardiac rehabilitation. Mood disorders such as depression are known to be highly prevalent in cardiac patients and to have a negative impact on the progression of coronary heart disease. However, cardiac patients have difficulties to get psychological treatments due to low availability and motivational difficulties. Web-based interventions have been proven to be effective in treating depressive symptoms. Deprexis is a promising web-based psychological treatment which was devised for depressed patients. The aim of the study InterHerz is to examine if Deprexis is an effective psychological treatment to reduce stress and depression in cardiac patients.

Symptomatic management of fever by Swiss board-certified pediatricians: results from a cross-sectional, Web-based survey

Symptomatic management is often all that is recommended in children with fever. To date, only 2 nationwide surveys of pediatricians regarding their attitudes toward fever have been published.

Can a novel web-based computer test predict poor simulated driving performance? A pilot study with healthy and cognitive-impaired participants

BACKGROUND Driving a car is a complex instrumental activity of daily living and driving performance is very sensitive to cognitive impairment. The assessment of driving-relevant cognition in older drivers is challenging and requires reliable and valid tests with good sensitivity and specificity to predict safe driving. Driving simulators can be used to test fitness to drive. Several studies have found strong correlation between driving simulator performance and on-the-road driving. However, access to driving simulators is restricted to specialists and simulators are too expensive, large, and complex to allow easy access to older drivers or physicians advising them. An easily accessible, Web-based, cognitive screening test could offer a solution to this problem. The World Wide Web allows easy dissemination of the test software and implementation of the scoring algorithm on a central server, allowing generation of a dynamically growing database with normative values and ensures that all users have access to the same up-to-date normative values. OBJECTIVE In this pilot study, we present the novel Web-based Bern Cognitive Screening Test (wBCST) and investigate whether it can predict poor simulated driving performance in healthy and cognitive-impaired participants. METHODS The wBCST performance and simulated driving performance have been analyzed in 26 healthy younger and 44 healthy older participants as well as in 10 older participants with cognitive impairment. Correlations between the two tests were calculated. Also, simulated driving performance was used to group the participants into good performers (n=70) and poor performers (n=10). A receiver-operating characteristic analysis was calculated to determine sensitivity and specificity of the wBCST in predicting simulated driving performance. RESULTS The mean wBCST score of the participants with poor simulated driving performance was reduced by 52%, compared to participants with good simulated driving performance (P<.001). The area under the receiver-operating characteristic curve was 0.80 with a 95% confidence interval 0.68-0.92. CONCLUSIONS When selecting a 75% test score as the cutoff, the novel test has 83% sensitivity, 70% specificity, and 81% efficiency, which are good values for a screening test. Overall, in this pilot study, the novel Web-based computer test appears to be a promising tool for supporting clinicians in fitness-to-drive assessments of older drivers. The Web-based distribution and scoring on a central computer will facilitate further evaluation of the novel test setup. We expect that in the near future, Web-based computer tests will become a valid and reliable tool for clinicians, for example, when assessing fitness to drive in older drivers.

3D Face Reconstruction from 2D Pictures: First Results of a Web-Based Computer Aided System for Aesthetic Procedures

The human face is a vital component of our identity and many people undergo medical aesthetics procedures in order to achieve an ideal or desired look. However, communication between physician and patient is fundamental to understand the patient’s wishes and to achieve the desired results. To date, most plastic surgeons rely on either “free hand” 2D drawings on picture printouts or computerized picture morphing. Alternatively, hardware dependent solutions allow facial shapes to be created and planned in 3D, but they are usually expensive or complex to handle. To offer a simple and hardware independent solution, we propose a web-based application that uses 3 standard 2D pictures to create a 3D representation of the patient’s face on which facial aesthetic procedures such as filling, skin clearing or rejuvenation, and rhinoplasty are planned in 3D. The proposed application couples a set of well-established methods together in a novel manner to optimize 3D reconstructions for clinical use. Face reconstructions performed with the application were evaluated by two plastic surgeons and also compared to ground truth data. Results showed the application can provide accurate 3D face representations to be used in clinics (within an average of 2 mm error) in less than 5 min.