PredictProtein—an open resource for online prediction of protein structural and functional features
By Guy Yachdav, Edda Kloppmann, László Kaján, M. Hecht, Tatyana Goldberg, Tobias Hamp, Peter Hönigschmid, Andrea Schafferhans, Manfred Roos, Michael Bernhofer and 10 more. Nucleic Acids Res., 2014
539 citations recorded by the source corpus.
PredictProtein is a meta-service for sequence analysis that has been predicting structural and functional features of proteins since 1992. Queried with a protein sequence it returns: multiple sequence alignments, predicted aspects of structure (secondary structure, solvent accessibility, transmembrane helices (TMSEG) and strands, coiled-coil regions, disulfide bonds and disordered regions) and function. The service incorporates analysis methods for the identification of functional regions (ConSurf), homology-based inference of Gene Ontology terms (metastudent), comprehensive subcellular localization prediction (LocTree3), protein–protein binding sites (ISIS2), protein–polynucleotide binding sites (SomeNA) and predictions of the effect of point mutations (non-synonymous SNPs) on protein function (SNAP2). Our goal has always been to develop a system optimized to meet the demands of experimentalists not highly experienced in bioinformatics. To this end, the PredictProtein results are presented as both text and a series of intuitive, interactive and visually appealing figures. The web server and sources are available at http://ppopen.rostlab.org.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/68bb5a865ee8e00689b02984a69cc415cf5aa6f6
Citations in the corpus
- The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis (2016, unknown): “fr], the PredictProtein server [(3); https: //www.”
- LocTree3 prediction of localization (2014, unknown): “If available, the result is returned immediately (minus queue waiting time); if not, the server retrieves a PSI-BLAST profile through the PredictProtein pipeline (19,20).”
- MSAViewer: interactive JavaScript visualization of multiple sequence alignments (2016, unknown): “Filled red rectangles indicate sequence annotations provided by the user [here: secondary structure predictions of PredictProtein (Yachdav et al. , 2014)].”
- The s2D method: simultaneous sequence-based prediction of the statistical populations of ordered and disordered regions in proteins. (2015, unknown): “Predictions of intrinsic disorder can be presented together with predictions of secondary or tertiary structure, as performed by some Web servers [22,26,27], to provide qualitative insights about the type and the stability of the structures formed by a given protein.”
- Structured states of disordered proteins from genomic sequences (2016, unknown): “Similarly, we identified propensity towards secondary structures in disordered proteins without relying on standard secondary structure prediction methods (Yachdav et al., 2014) as these are trained on predominantly ordered sequences.”
- Comprehensive review of methods for prediction of intrinsic disorder and its molecular functions (2017, unknown): “This method is a part of a comprehensive PredictProtein Open platform [96] for the prediction of protein structure and function.”