The glass transition of thin polymer films in relation to the interfacial dynamics.

As opposed to measurements on the glass transition of a polymer in the bulk, measurements of thin polymer layers reflect--due to the alterations of the glassy dynamics at the confining interfaces--several contributions acting together to give the net response of a polymer film. This fundamental difference is exemplified in detail for the particular case of broadband dielectric spectroscopy, an experimental tool extensively employed to investigate the glassy dynamics of polymers under condition of geometrical confinement.

FireDB--a database of functionally important residues from proteins of known structure.

The FireDB database is a databank for functional information relating to proteins with known structures. It contains the most comprehensive and detailed repository of known functionally important residues, bringing together both ligand binding and catalytic residues in one site. The platform integrates biologically relevant data filtered from the close atomic contacts in Protein Data Bank crystal structures and reliably annotated catalytic residues from the Catalytic Site Atlas. The interface allows users to make queries by protein, ligand or keyword. Relevant biologically important residues are displayed in a simple and easy to read manner that allows users to assess binding site similarity across homologous proteins. Binding site residue variations can also be viewed with molecular visualization tools. The database is available at http://firedb.bioinfo.cnio.es.

Empirical limits for template-based protein structure prediction: the CASP5 example.

Most protein structure prediction methods use templates to assist in the construction of protein models. In this paper, we analyse the current state of template-based modelling approaches and reach an estimate of the empirical limits of these methods. Our analysis show that current prediction methods are already reaching these empirical accuracy limits in the easier cases, where finding a close homologue to the native target structure is not a problem. However, we find that even in the absence of alignment errors and using optimal templates, template-based methods have intrinsic limitations, suggesting that other methodologies, such as ab initio procedures, must be used if accuracy is ultimately to be improved.

Evaluation of travoprost as adjunctive therapy in patients with uncontrolled intraocular pressure while using timolol 0.5%.

PURPOSE: To evaluate the intraocular pressure-lowering efficacy and safety of travoprost 0.0015% and 0.004%, dosed daily in the evening compared with vehicle, in patients with open-angle glaucoma or ocular hypertension, whose intraocular pressure was not adequately controlled on timolol 0.5% twice daily (twice daily). METHODS: Subjects who qualified at screening began a run-in period dosing timolol twice daily for 3 weeks. If the subjects had an intraocular pressure of 24 to 36 mm Hg at 8 AM and 21 to 36 mm Hg at 10 AM and 4 pm in at least one eye on timolol, they were randomized to one of two concentrations of travoprost (0.0015% or 0.004%) or vehicle solution every day and were followed for 6 months. Four hundred twenty-six subjects were randomized. The mean intraocular pressure at 8 AM, 10 AM, and 4 PM in the patient's eye with the higher intraocular pressure was used for the analysis. RESULTS: Mean baseline values (25 mm Hg) for subjects at eligibility (while maintained on timolol) were not significantly different (P <.0001) among the treatment groups. The intraocular pressure was lowered an additional -5.7 to -7.2 mm Hg and -5.1 to -6.7 mm Hg in the travoprost 0.004% and 0.0015% concentrations, respectively. These changes were significantly (P < or =.0001) different from the vehicle group (-1.3 to -2.8 mm Hg). The intraocular pressure range on treatment at all visit times over the 6-month treatment period ranged from 17.9 to 19.2 mm Hg for travoprost 0.004% and 18.3 to 20.1 mm Hg for travoprost 0.0015% compared with 22.4 to 24.1 mm Hg for vehicle. Average hyperemia scores ranged from trace to mild (mean 0.5 on a scale of 0 = none/trace; 1= mild; 2 = moderate; 3 = severe) for all treatment groups. No iris pigmentation changes were observed in any patient during this study. There were no clinically or statistically significant changes from baseline in visual acuity, ocular cells and flare, fundus parameter, cup-to-disk ratio and visual field between the treatment groups. There were no serious adverse events reported for any treatment group. CONCLUSIONS: Travoprost produced clinically relevant and statistically significant additional intraocular pressure reductions from baseline when used adjunctively with timolol in subjects with open-angle glaucoma or ocular hypertension.

Successful recognition of protein folds using threading methods biased by sequence similarity and predicted secondary structure.

Analysis of our fold recognition results in the 3rd Critical Assessment in Structure Prediction (CASP3) experiment, using the programs THREADER 2 and GenTHREADER, shows an encouraging level of overall success. Of the 23 submitted predictions, 20 targets showed no clear sequence similarity to proteins of known 3D structure. These 20 targets can be divided into 22 domains, of which, 20 domains either entirely match a previously known fold, or partially match a substantial region of a known fold. Of these 20 domains, we correctly assigned the folds in 10 cases.