Protein design is a powerful tool for elucidating mechanisms of function and engineering new therapeutics and nanotechnologies. Although soluble protein design has advanced, membrane protein design remains challenging because of difficulties in modeling the lipid bilayer. In this work, we developed an ...
Protein Domain Prediction Crystallography Phase Determination EM Data Processing and Interpretation NMR Data Processing and Interpretation Combining X-ray Crystallography and Solution NMR Data Image and Data Analysis Integrative Structural Biology Services+ Model Reconstruction of Crystal Structures Using Cryo-...
Creators of novel prediction methods can use this benchmark server to evaluate the performance of their new methods. The benchmark server will be a valuable tool for researchers seeking to extract more sophisticated information from the large and growing protein sequence databases....
the experimental study of proteins remains difficult. Considerable efforts have thus been made to develop prediction methods. Most of these were conceived to detect transmembrane helices in polytopic proteins. Alternatively, a membrane protein can be monotopic and anchoredviaan...
Membrane protein prediction was achieved using the DAVID Bioinformatics Resources (http://david.abcc.ncifcrf.gov/)(42) and the Gene Ontology (GO) annotation (www.geneontology.org) and the TransMembrane Hidden Markov Model (TMHMM, http://www.cbs.dtu.dk/services/TMHMM/). We used PANTHER (...
(Supplementary Fig.2b, c). Subsequently, we utilized these selected PPI templates to infer MP-interacting protein candidates by evaluating theirSSIMvalues by searching the complete human proteome database (UniProt12; Supplementary Fig.2d). We compared the PPI prediction accuracies of ourSSIM, six ...
resulting in designs with identical length and identical functional sites. For the design of the active conformation, we found that it was not possible to generate high-confidence designs without the presence of G protein; hence, gradient descent and prediction were performed in the presence of the...
If the functional consequences of protein shedding were not clarified in the original studies, the shed membrane protein was then categorized based on the function description or annotation in the UniProtKB/Swiss-Prot database. Incorporated shedding predictor ShedP The in-house prediction tool ShedP ...
The epithelial membrane protein (EMP2) was identified as one of the up-regulated genes by isoflavones. EMP2 overexpression suppressed foci formation, anchorage-independent growth in vitro, and tumorigenicity in severe combined immunodeficiency mice (all P < 0.05). In addition, a cross-talk between...
In the prediction with the IUPred tool, the residues of the S protein predicted with disorder prediction score higher than 0.2 were considered unstructured. Surface accessibility was predicted with two tools, BepiPred-2.0 providing the probability of exposed residues and the method of Emini providing...