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
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:
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.
How to search PDBe (Protein Data Bank - Europe)
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 University, University of San Diego Supercomputer Center, University of San Francisco
Supporting Institutions: National Science Foundation, National Institutes of Health, US Department of Energy Office of Science
Tutorials:
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 Technology, Uppsala University, Science for Life Laboratory
Supporting Institution(s): Elixir, Knut & Alice Wallenberg Foundation
Tutorials:
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 Bioinformatics, Novo Nordisk Foundation Center for Protein Research, European Molecular Biology Laboratory - Heidelberg, University of Zurich
Tutorials:
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 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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