Scoring docking conformations using predicted protein interfaces

BACKGROUND: Since proteins function by interacting with other molecules, analysis of protein-protein interactions is essential for comprehending biological processes. Whereas understanding of atomic interactions within a complex is especially useful for drug design, limitations of experimental techniques have restricted their practical use. Despite progress in docking predictions, there is still room for improvement. In this study, we contribute to this topic by proposing T-PioDock, a framework for detection of a native-like docked complex 3D structure. T-PioDock supports the identification of near-native conformations from 3D models that docking software produced by scoring those models using binding interfaces predicted by the interface predictor, Template based Protein Interface Prediction (T-PIP). RESULTS: First, exhaustive evaluation of interface predictors demonstrates that T-PIP, whose predictions are customised to target complexity, is a state-of-the-art method. Second, comparative study between T-PioDock and other state-of-the-art scoring methods establishes T-PioDock as the best performing approach. Moreover, there is good correlation between T-PioDock performance and quality of docking models, which suggests that progress in docking will lead to even better results at recognising near-native conformations. CONCLUSION: Accurate identification of near-native conformations remains a challenging task. Although availability of 3D complexes will benefit from template-based methods such as T-PioDock, we have identified specific limitations which need to be addressed. First, docking software are still not able to produce native like models for every target. Second, current interface predictors do not explicitly consider pairwise residue interactions between proteins and their interacting partners which leaves ambiguity when assessing quality of complex conformations

Crystal structure of mouse RhoA:GTPcS complex in a centered lattice

10.1007/s10969-012-9143-5Journal of Structural and Functional Genomics134241-245JSFG

Treatment of primary varicose veins by endovenous obliteration with the VNUS closure system: Results of a prospective multicentre study

Background. Radio frequency obliteration of the saphenous veins has been introduced as a less invasive alternative to traditional surgery for varicose veins. Objective. To report the efficacy of obliteration and clinical outcomes following endovenous obliteration of the saphenous vein with limited follow-up to 3 years. Materials and methods. Radiofreq uency obliteration (Closure® system, VNUS Medical Technologies, San Jose, CA) was performed in 330 limbs of 294 patients in a prospective worldwide multicentre study with 31 participating sites. Follow-up duplex ultrasound and clinical examinations were performed at annual intervals. The main outcome measures were the completeness of occlusion of the treated vein segment, presence of reflux and presence of signs and symptoms of venous disease. Results. Before treatment 3.9% of limbs were categorised as CEAP clinical class zero or one. This improved to 82.9% at 1 year, 83.1% at 2 years and 86.8% at 3 years following treatment. Varicose vein free rates were 1 year: 90.1%, 2 years: 87.2%, 3 years: 88.2%. Duplex ultrasound demonstrated a reflux-free rate of about 88% over 3 years. Total occlusion (TO) of veins was 1 year: 81%, 2 years: 80.4% and 3 years: 75%. Partial occlusion (PO, 5 cm open segment) was 1 year: 12.7%, 2 years: 12.2% and 3 years: 7.4%. Partial occlusion did not result in any differences in the symptom severity score, the number of symptom free limbs, or the varicose vein absence rates at any follow-up time point when compared to the total occlusion group. The varicose vein absence rates were significantly lower in the IO group comparing to the TO and PO groups. Conclusions. Radiofrequency saphenous vein obliteration improves the symptoms of varicose veins. The reflux-free rates in the treated veins remain constant over a 3 year follow-up period. There is no difference in clinical outcomes between the TO and the PO limbs, suggesting clinical effectiveness of the PO category. Greater than a 5 cm open segment in treated veins poses a risk of recurrence. © 2004 Elsevier Ltd. All rights reserved