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We introduce two GALAXY web servers called GalaxySite and GalaxyPepDock that predict protein complex structures with small organic compounds and peptides, respectively. GalaxySite predicts ligands that may bind the input protein and generates complex structures of the protein with the predicted ligands from the protein structure given as input or predicted(More)
The CAPRI (Critical Assessment of Predicted Interactions) and CASP (Critical Assessment of protein Structure Prediction) experiments have demonstrated the power of community-wide tests of methodology in assessing the current state of the art and spurring progress in the very challenging areas of protein docking and structure prediction. We sought to bring(More)
Protein-peptide interactions are involved in a wide range of biological processes and are attractive targets for therapeutic purposes because of their small interfaces. Therefore, effective protein-peptide docking techniques can provide the basis for potential therapeutic applications by enabling an atomic-level understanding of protein interactions. With(More)
Community-wide blind prediction experiments such as CAPRI and CASP provide an objective measure of the current state of predictive methodology. Here we describe a community-wide assessment of methods to predict the effects of mutations on protein-protein interactions. Twenty-two groups predicted the effects of comprehensive saturation mutagenesis for two(More)
SUMMARY A large number of proteins function as homo-oligomers; therefore, predicting homo-oligomeric structure of proteins is of primary importance for understanding protein function at the molecular level. Here, we introduce a web server for prediction of protein homo-oligomer structure. The server takes a protein monomer structure as input and predicts(More)
We report the first assessment of blind predictions of water positions at protein-protein interfaces, performed as part of the critical assessment of predicted interactions (CAPRI) community-wide experiment. Groups submitting docking predictions for the complex of the DNase domain of colicin E2 and Im2 immunity protein (CAPRI Target 47), were invited to(More)
A computational protein-protein docking method that predicts atomic details of protein-protein interactions from protein monomer structures is an invaluable tool for understanding the molecular mechanisms of protein interactions and for designing molecules that control such interactions. Compared to low-resolution docking, high-resolution docking explores(More)
We present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein-protein docking communities. The Round comprised 25 targets from amongst those submitted for the CASP11 prediction experiment of 2014. The targets included mostly homodimers, a few homotetramers,(More)
People should feel more immersive and act realistically when the backgrounds of virtual reality system are more similar to real world. If we surround users by the real images-panoramic imaging-in CAVE, we can make more realistic environment. We make the panoramic images from the real environment using a digital camera and a panoramic tripod head and apply(More)
In this paper, the panoramic stereo images are produced from the real environment using a digital camera and a panoramic tripod head. And they are applied to the CAVE system as panoramic stereo background to increase user's immersion. The images for left and right eye are taken and stitched separately for stereo imaging. Finally the stereo backgrounds are(More)