title: PredictProtein--an open resource for online prediction of protein structural and functional features.
abstract: 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.
authors.affiliation: Department of Informatics, Bioinformatics & Computational Biology i12, TUM (Technische Universität München), Garching/Munich 85748, Germany Biosof LLC, New York, NY 10001, USA TUM Graduate School, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), TUM (Technische Universität München), Garching/Munich 85748, Germany gyachdav@rostlab.org.
authors.forename: Guy
authors.initials: G
authors.lastname: Yachdav
authors.affiliation: Department of Informatics, Bioinformatics & Computational Biology i12, TUM (Technische Universität München), Garching/Munich 85748, Germany New York Consortium on Membrane Protein Structure (NYCOMPS), Columbia University, New York, NY 10032, USA.
authors.forename: Edda
authors.initials: E
authors.lastname: Kloppmann
authors.affiliation: Department of Informatics, Bioinformatics & Computational Biology i12, TUM (Technische Universität München), Garching/Munich 85748, Germany.
authors.forename: Laszlo
authors.initials: L
authors.lastname: Kajan
authors.affiliation: Department of Informatics, Bioinformatics & Computational Biology i12, TUM (Technische Universität München), Garching/Munich 85748, Germany TUM Graduate School, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), TUM (Technische Universität München), Garching/Munich 85748, Germany.
authors.forename: Maximilian
authors.initials: M
authors.lastname: Hecht
authors.affiliation: Department of Informatics, Bioinformatics & Computational Biology i12, TUM (Technische Universität München), Garching/Munich 85748, Germany TUM Graduate School, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), TUM (Technische Universität München), Garching/Munich 85748, Germany.
authors.forename: Tatyana
authors.initials: T
authors.lastname: Goldberg
authors.affiliation: Department of Informatics, Bioinformatics & Computational Biology i12, TUM (Technische Universität München), Garching/Munich 85748, Germany.
authors.forename: Tobias
authors.initials: T
authors.lastname: Hamp
authors.affiliation: Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, Freising 85354, Germany.
authors.forename: Peter
authors.initials: P
authors.lastname: Hönigschmid
authors.affiliation: Department of Informatics, Bioinformatics & Computational Biology i12, TUM (Technische Universität München), Garching/Munich 85748, Germany.
authors.forename: Andrea
authors.initials: A
authors.lastname: Schafferhans
authors.affiliation: Department of Informatics, Bioinformatics & Computational Biology i12, TUM (Technische Universität München), Garching/Munich 85748, Germany.
authors.forename: Manfred
authors.initials: M
authors.lastname: Roos
authors.affiliation: Department of Informatics, Bioinformatics & Computational Biology i12, TUM (Technische Universität München), Garching/Munich 85748, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Bernhofer
authors.affiliation: Department of Informatics, Bioinformatics & Computational Biology i12, TUM (Technische Universität München), Garching/Munich 85748, Germany.
authors.forename: Lothar
authors.initials: L
authors.lastname: Richter
authors.affiliation: The Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Tel Aviv, Israel.
authors.forename: Haim
authors.initials: H
authors.lastname: Ashkenazy
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK Institute for Food and Plant Sciences WZW-Weihenstephan, Alte Akademie 8, Freising 85350, Germany.
authors.forename: Marco
authors.initials: M
authors.lastname: Punta
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire, CB10 1SD, UK.
authors.forename: Avner
authors.initials: A
authors.lastname: Schlessinger
authors.affiliation: Biosof LLC, New York, NY 10001, USA Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA.
authors.forename: Yana
authors.initials: Y
authors.lastname: Bromberg
authors.affiliation: Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA.
authors.forename: Reinhard
authors.initials: R
authors.lastname: Schneider
authors.affiliation: Luxembourg University & Luxembourg Centre for Systems Biomedicine, 4362 Belval, Luxembourg.
authors.forename: Gerrit
authors.initials: G
authors.lastname: Vriend
authors.affiliation: CMBI, NCMLS, Radboudumc Nijmegen Medical Centre, 6525 GA Nijmegen, The Netherlands.
authors.forename: Chris
authors.initials: C
authors.lastname: Sander
authors.affiliation: Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, 10065 NY, USA.
authors.forename: Nir
authors.initials: N
authors.lastname: Ben-Tal
authors.affiliation: Department of Informatics, Bioinformatics & Computational Biology i12, TUM (Technische Universität München), Garching/Munich 85748, Germany Biosof LLC, New York, NY 10001, USA New York Consortium on Membrane Protein Structure (NYCOMPS), Columbia University, New York, NY 10032, USA The Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Tel Aviv, Israel Department of Biochemistry and Molecular Biophysics & New York Consortium on Membrane Protein Structure (NYCOMPS), Columbia University, New York, NY 10032, USA Institute for Advanced Study (TUM-IAS), Garching/Munich 85748, Germany.
authors.forename: Burkhard
authors.initials: B
authors.lastname: Rost
mesh_terms: D019943:Amino Acid Substitution; D001665:Binding Sites; D063990:Gene Ontology; D020407:Internet; D064267:Intrinsically Disordered Proteins / Q000737:chemistry; D008565:Membrane Proteins / Q000737:chemistry; D009154:Mutation; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D011506:Proteins / Q000032:analysis / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D017386:Sequence Homology, Amino Acid; D012984:Software
chemical_list: D064267:Intrinsically Disordered Proteins; D008565:Membrane Proteins; D011506:Proteins