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Penev PI, McCann HM, Meade CD, Alvarez-Carreño C, Maddala A, Bernier CR, Chivukula VL, Ahmad M, Gulen B, Sharma A, Williams LD, Petrov AS. ProteoVision: web server for advanced visualization of ribosomal proteins. Nucleic Acids Res 2021; 49:W578-W588. [PMID: 33999189 PMCID: PMC8265156 DOI: 10.1093/nar/gkab351] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/11/2021] [Accepted: 04/21/2021] [Indexed: 11/26/2022] Open
Abstract
ProteoVision is a web server designed to explore protein structure and evolution through simultaneous visualization of multiple sequence alignments, topology diagrams and 3D structures. Starting with a multiple sequence alignment, ProteoVision computes conservation scores and a variety of physicochemical properties and simultaneously maps and visualizes alignments and other data on multiple levels of representation. The web server calculates and displays frequencies of amino acids. ProteoVision is optimized for ribosomal proteins but is applicable to analysis of any protein. ProteoVision handles internally generated and user uploaded alignments and connects them with a selected structure, found in the PDB or uploaded by the user. It can generate de novo topology diagrams from three-dimensional structures. All displayed data is interactive and can be saved in various formats as publication quality images or external datasets or PyMol Scripts. ProteoVision enables detailed study of protein fragments defined by Evolutionary Classification of protein Domains (ECOD) classification. ProteoVision is available at http://proteovision.chemistry.gatech.edu/.
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Affiliation(s)
- Petar I Penev
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Holly M McCann
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Caeden D Meade
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Claudia Alvarez-Carreño
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Aparna Maddala
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Chad R Bernier
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Vasanta L Chivukula
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Maria Ahmad
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Burak Gulen
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Aakash Sharma
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Loren Dean Williams
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Anton S Petrov
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
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