Inelastic neutron scattering is a form of vibrational spectroscopy for which the measured scattering intensities are directly related to vibrational amplitudes, allowing, in principle, convenient comparison with theoretical dynamical models. However, until recently, neutron sources and instruments have not allowed spectra to be collected on globular proteins with useful energy resolutions in the frequency range of most macromolecular vibrations (∼50−3500 cm-1). The construction of the time-focussing crystal analyzer (TFXA) spectrometer at the ISIS pulsed neutron source near Oxford has changed this situation, allowing high-resolution spectra to be obtained over the whole frequency range of interest. We present here TFXA vibrational spectra of the enzyme, Staphylococcal nuclease, and compare the results with spectra calculated from a normal mode analysis of the protein using the program CHARMM (see ref ). The calculated spectral intensities, which were obtained using a force field that was not refined to fit the present experimental data, are in general agreement with experiment and are used to assign the peaks.

We describe the methodology and results from our participation in the second Antibody Modeling Assessment experiment. During the experiment we predicted the structure of eleven unpublished antibody Fv fragments. Our prediction methods centered on template-based modeling; potential templates were selected from an antibody database based on their sequence similarity to the target in the framework regions. Depending on the quality of the templates, we constructed models of the antibody framework regions either using a single, chimeric or multiple template approach. The hypervariable loop regions in the initial models were rebuilt by grafting the corresponding regions from suitable templates onto the model. For the H3 loop region, we further refined models using ab initio methods. The final models were subjected to constrained energy minimization to resolve severe local structural problems. The analysis of the models submitted show that Accelrys tools allow for the construction of quite accurate models for the framework and the canonical CDR regions, with RMSDs to the X-ray structure on average below 1 Å for most of these regions. The results show that accurate prediction of the H3 hypervariable loops remains a challenge. Furthermore, model quality assessment of the submitted models show that the models are of quite high quality, with local geometry assessment scores similar to that of the target X-ray structures. Proteins 2014; 82:1583–1598. © 2014 The Authors. Proteins published by Wiley Periodicals, Inc.