ReFOLD: a server for the refinement of 3D protein models guided by accurate quality estimates

ReFOLD is a novel hybrid refinement server with integrated high performance global and local Accuracy Self Estimates (ASEs). The server attempts to identify and to fix likely errors in user supplied 3D models of proteins via successive rounds of refinement. The server is unique in providing output for multiple alternative refined models in a way that allows users to quickly visualize the key residue locations, which are likely to have been improved. This is important, as global refinement of a full chain model may not always be possible, whereas local regions, or individual domains, can often be much improved. Thus, users may easily compare the specific regions of the alternative refined models in which they are most interested e.g. key interaction sites or domains. ReFOLD was used to generate hundreds of alternative refined models for the CASP12 experiment, boosting our group's performance in the main tertiary structure prediction category. Our successful refinement of initial server models combined with our built-in ASEs were instrumental to our second place ranking on Template Based Modeling (TBM) and Free Modeling (FM)/TBM targets. The ReFOLD server is freely available at: http://www.reading.ac.uk/bioinf/ReFOLD/

IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences

IntFOLD is an independent web server that integrates our leading methods for structure and function prediction. The server provides a simple unified interface that aims to make complex protein modelling data more accessible to life scientists. The server web interface is designed to be intuitive and integrates a complex set of quantitative data, so that 3D modelling results can be viewed on a single page and interpreted by non-expert modellers at a glance. The only required input to the server is an amino acid sequence for the target protein. Here we describe major performance and user interface updates to the server, which comprises an integrated pipeline of methods for: tertiary structure prediction, global and local 3D model quality assessment, disorder prediction, structural domain prediction, function prediction and modelling of protein-ligand interactions. The server has been independently validated during numerous CASP (Critical Assessment of Techniques for Protein Structure Prediction) experiments, as well as being continuously evaluated by the CAMEO (Continuous Automated Model Evaluation) project. The IntFOLD server is available at: http://www.reading.ac.uk/bioinf/IntFOLD

IntFOLD: an integrated web resource for high performance protein structure and function prediction

The IntFOLD server provides a unified resource for the automated prediction of: protein tertiary structures with built-in estimates of model accuracy (EMA), protein structural domain boundaries, natively unstructured or disordered regions in proteins, and protein–ligand interactions. The component methods have been independently evaluated via the successive blind CASP experiments and the continual CAMEO benchmarking project. The IntFOLD server has established its ranking as one of the best performing publicly available servers, based on independent official evaluation metrics. Here, we describe significant updates to the server back end, where we have focused on performance improvements in tertiary structure predictions, in terms of global 3D model quality and accuracy self-estimates (ASE), which we achieve using our newly improved ModFOLD7 rank algorithm. We also report on various upgrades to the front end including: a streamlined submission process, enhanced visualization of models, new confidence scores for ranking, and links for accessing all annotated model data. Furthermore, we now include an option for users to submit selected models for further refinement via convenient push buttons

Effect of early clinical skills teaching on 3rd year medical students' learning: The student perspective

AbstractObjectivesThe main purpose of the early introduction of Clinical Skills Learning (CSL) to pre-clinical years is to allow medical students to gain experience in clinical examination skills, basic medical procedures, history-taking and clinical communication. The objective of this study was to determine the effectiveness of the early teaching of clinical skills in preparing medical students for their clinical years.MethodsA validated questionnaire assessing the value of CSL on students in their first clinical year was distributed to 3rd year medical students. The questionnaire consisted of 8 items with a five-point Likert scale and one open-ended question.ResultsThe response rate to the questionnaire was approximately 62%. Nearly 97 (70.8%) students suggested that CSL was a favourable teaching strategy. A high percentage of students (90.5%) agreed that CSL was a useful pre-clinical module to prepare them for their clinical years. The students gave positive feedback on the teaching of history-taking and physical examination, exposure to the hospital environment and acquisition of communication skills with supervisors and patients. No student perceived the CSL module as poor.ConclusionsEarly CSL was well-perceived by students in preparing them for their clinical years. CSL is a vital part of the pre-clinical curriculum and should be further enriched with frequent hospital visits to enhance students' confidence level and performance when interacting with patients during their clinical years

Physical function assessment of older adults with lower body fractures at 3 months post-discharge from hospital

Nurul ‘Izzah Ibrahim,1 Mohd Sharkawi Ahmad,1 Mohamed S Zulfarina,1 Sharifah Nurul Aqilah Sayed Mohd Zaris,2 Zainal Abidin Nor Azlin,3 Isa Naina Mohamed,1 Norazlina Mohamed,1 Sabarul Afian Mokhtar,2 Ahmad Nazrun Shuid1 1Department of Pharmacology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia; 2Department of Orthopedics and Traumatology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia; 3Department of Orthopedics & Traumatology, Hospital Kuala Lumpur, Kuala Lumpur, Malaysia Background and purpose: Physical function assessment can be performed to assess functional mobility among older adults, especially after a traumatic incident such as lower body fracture (LBF). The objective of this study was to evaluate physical function of older patients with LBF after 3 months of discharge from the hospital. Patients and methods: A total of 89 patients were followed up at the discharge phase. Four independent variables were tested: age, sex, type of fracture, and use of a walking aid before fracture. Mobility and strength were assessed with the Timed Up and Go (TUG) test and handgrip strength (HGS) test, respectively.  Results: The majority of the patients were ≥65 years old (64%), female (61.8%), of Chinese ethnicity (50.6%), and had a hip fracture (51.7%). The mean time for TUG test was 26.11 seconds, while mean HGS was 19.02 kg. We found significant differences in TUG test scores with respect to all independent variables tested: age (P=0.026), sex (P=0.011), fracture type (P<0.001), and use of a walking aid before fracture (P=0.004). Significant differences were also detected in HGS test scores with respect to all independent variables tested: age (P<0.001), sex (P<0.001), fracture type (P<0.001), and use of a walking aid before fracture (P=0.035). Conclusion: Increasing age, female sex, having a hip fracture, and use of a walking aid before fracture predicted reduction in the physical function and strength among older adults with LBF. Keywords: lower body fracture, Timed Up and Go test, handgrip strength test, rehabilitatio