PredictProtein--an open resource for online prediction of protein structural and functional features

Guy Yachdav; Edda Kloppmann; Laszlo Kajan; Maximilian Hecht; Tatyana Goldberg; Tobias Hamp; Peter Hönigschmid; Andrea Schafferhans; Manfred Roos; Michael Bernhofer; Lothar Richter; Haim Ashkenazy; Marco Punta; Avner Schlessinger; Yana Bromberg; Reinhard Schneider; Gerrit Vriend; Chris Sander; Nir Ben-Tal; Burkhard Rost

doi:10.1093/nar/gku366

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PredictProtein--an open resource for online prediction of protein structural and functional features

Journal article

Open access

Peer reviewed

PredictProtein--an open resource for online prediction of protein structural and functional features

Guy Yachdav, Edda Kloppmann, Laszlo Kajan, Maximilian Hecht, Tatyana Goldberg, Tobias Hamp, Peter Hönigschmid, Andrea Schafferhans, Manfred Roos, Michael Bernhofer, …

Nucleic acids research, Vol.42(Web Server issue), pp.W337-43

07/2014

DOI: https://doi.org/10.1093/nar/gku366

PMCID: PMC4086098

PMID: 24799431

Abstract

Amino Acid Substitution

Binding Sites

Gene Ontology

Internet

Intrinsically Disordered Proteins - chemistry

Membrane Proteins - chemistry

Mutation

Protein Conformation

Protein Interaction Mapping

Proteins - analysis

Proteins - genetics

Proteins - metabolism

Sequence Alignment

Sequence Analysis, Protein

Sequence Homology, Amino Acid

Software

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.

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Title: PredictProtein--an open resource for online prediction of protein structural and functional features
Creators: Guy Yachdav - 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
Edda Kloppmann - 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
Laszlo Kajan - Department of Informatics, Bioinformatics & Computational Biology i12, TUM (Technische Universität München), Garching/Munich 85748, Germany
Maximilian Hecht - 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
Tatyana Goldberg - 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
Tobias Hamp - Department of Informatics, Bioinformatics & Computational Biology i12, TUM (Technische Universität München), Garching/Munich 85748, Germany
Peter Hönigschmid - Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, Freising 85354, Germany
Andrea Schafferhans - Department of Informatics, Bioinformatics & Computational Biology i12, TUM (Technische Universität München), Garching/Munich 85748, Germany
Manfred Roos - Department of Informatics, Bioinformatics & Computational Biology i12, TUM (Technische Universität München), Garching/Munich 85748, Germany
Michael Bernhofer - Department of Informatics, Bioinformatics & Computational Biology i12, TUM (Technische Universität München), Garching/Munich 85748, Germany
Lothar Richter - Department of Informatics, Bioinformatics & Computational Biology i12, TUM (Technische Universität München), Garching/Munich 85748, Germany
Haim Ashkenazy - The Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Tel Aviv, Israel
Marco Punta - Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK Institute for Food and Plant Sciences WZW-Weihenstephan, Alte Akademie 8, Freising 85350, Germany
Avner Schlessinger - European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire, CB10 1SD, UK
Yana Bromberg - 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
Reinhard Schneider - Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
Gerrit Vriend - Luxembourg University & Luxembourg Centre for Systems Biomedicine, 4362 Belval, Luxembourg
Chris Sander - CMBI, NCMLS, Radboudumc Nijmegen Medical Centre, 6525 GA Nijmegen, The Netherlands
Nir Ben-Tal - Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, 10065 NY, USA
Burkhard Rost - 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
Publication Details: Nucleic acids research, Vol.42(Web Server issue), pp.W337-43
Date published: 07/2014
Grant note: U54 GM095315 / NIGMS NIH HHS
Academic Unit: Biochemistry and Microbiology (SEBS)
Language: English
Resource Type: Journal article
Identifiers: 991031665673504646