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Bioinformatics: Proteomics Databases

neXtProt

netXtProt is a database of the human proteome containing information on over 20,000 human proteins, the vast majority of which their existence has been determined through direct identification or through the identification of their mRNA transcripts. neXtProt offers the ability to identify proteins through their name, DNA, amino acid sequence, and chromosome of origin. neXtProt also allows for the more in depth study of protein variants of ion channels, kinases, and proteins associated with cancer.

Link: https://www.nextprot.org/

Operating Institution: Swiss Institute of Bioinformatics 

Tutorials:

How to perform an simple search

How to perform an advanced search  

How to refine and interpret search results 

How to use analysis tools

Protopedia

Protopedia is a wiki style database containing information on a wide array of biological macromolecules. The site offers generalized information about the molecule of interest in addition to providing 3D visuals on the structure of the molecule and information on its interactions, locations, and targets. As a wiki style platform Protopedia allows for the community to add information based on their research and publications and seeks to provide the information in a way to aid others in research and facilitate the teaching of students. 

Link: http://proteopedia.org/wiki/index.php/Main_Page

Operating Institution(s): The Israel Structural Proteomics Center

Supporting Institution(s): Weizmann Institute of Science

Tutorials:

How to perform a search

General Help Page

Protein Data Bank

The Protein Data Bank is a database of proteins and nucleic acids. The site offerers scientists and educators the ability to both upload new information on known sequences and proteins or completely novel entities, and download sequence and other scientific information as well. The database allows for searching based on sequence, function, ligand, and drug targets as well as offering visual representations of the 3D structure of proteins, the pathways they are involved in, mechanism of drug and ligand interaction, and where their sequence lies on human chromosomes.

PLEASE check the molecule of the month for very god explanation of the different molecules and their purpose.

Example: https://pdb101.rcsb.org/browse

Link: https://www.rcsb.org/

Operating Institution(s): Rutgers UniversityUniversity of San Diego Supercomputer CenterUniversity of San Francisco

Supporting Institutions: National Science FoundationNational Institutes of HealthUS Department of Energy Office of Science

Tutorials:

Help Topics

Educators Guide and Resources for PDB

Human Protein Atlas

The Human Protein Atlas is a database containing the location of all known human proteins with three major sub-divisions. The Tissue Atlas showing the protein expression levels and their localization in all human tissues, the Cell Atlas shows the expression and sub-cellular localization of proteins in 64 human cell lines, the Pathology Atlas shows the abhorrent expression patterns of proteins in 18 different types of human cancers. In addition to these Atlases the database contains information on wide classes of human proteins, protocols and methods for human protein experimentation ,and access to antibodies and cell lines for research. 

Link: https://www.proteinatlas.org/

Operating Institution(s): KTH Royal Institute of TechnologyUppsala UniversityScience for Life Laboratory

Supporting Institution(s): ElixirKnut & Alice Wallenberg Foundation

Tutorials:

FAQ Page

STRING

STRING is a proteomic database focusing on the networks and interactions of proteins in a wide array of species. STRING allows for the searching of one or multiple proteins at a time with the ability to additionally limit the search to the desired species. STRING's results shows visual representations of the interactions that the searched protein is involved in along with expression, location, transcription, and experimental data on the protein and its associated proteins. 

Link: https://string-db.org/

Operating Institution(s): Swiss Institute of BioinformaticsNovo Nordisk Foundation Center for Protein ResearchEuropean Molecular Biology Laboratory - HeidelbergUniversity of Zurich

Tutorials:

FAQ Page

SuperPose

SuperPose is an online resource for the alignment of protein structural information in order to ascertain the degree of  structural similarity and superposition the proteins possess.

Link: http://wishart.biology.ualberta.ca/SuperPose/

Operating Institution(s): Wishart Research Group - University of Alberta 

Supporting Institution(s): Genome Alberta

Tutorials:

TopFIND

TopFIND is a database of N- and C- termini of proteins. The database provides information of the amino acid sequence of a multitude of proteins along with experimentally identified modifications to the N- and C- termini along with internal sequence and modification variation between species

Link: http://clipserve.clip.ubc.ca/topfind/

Operating Institution(s): Overall Lab - University of British Columbia

Tutorials: 

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