Resources

General

http://www.uniprot.org/ Uniprot provides a good summary of each protein’s available data. It also provides direct links to many other resource pages for that protein
https://www.ncbi.nlm.nih.gov/pubmed Pubmed allows for searches of abstracts and keywords across ALL journal articles. Using the Gene Name (or a synonym) to search pubmed could provide articles mentioning the protein of interest.
https://www.ncbi.nlm.nih.gov/pmc/ Pubmed Central (PMC) allows for searches of the full-text across FREE-ACCESS journal articles only. Using the Gene Name (or a synonym) to search PMC could provide articles mentioning the protein of interest anywhere in the manuscript including tables and figure legends. Check the tables in the paper for the Gene Name (or a synonym).
https://amp.pharm.mssm.edu/Harmonizome/ Search for proteins and their functional terms extracted and organized from over a hundred publicly available resources.
https://pharos.nih.gov/idg/index Pharos is the user interface to the Knowledge Management Center (KMC) for Illuminating the Druggable Genome.

Protein-Protein Interactions

http://string-db.org/ STRING is an awesome resource that brings together many types of data to provide connections between proteins. It may provide links between proteins of known function and your protein. It will look for associations in other species.
https://honiglab.c2b2.columbia.edu/PrePPI/ Aggregates different data sources with protein-protein interaction data/publications/predictions.
http://elm.eu.org/ Provides predictions for functional sites (protein binding or post-translational modification) within proteins
https://scansite4.mit.edu/ Provides predictions for functional sites (protein binding or post-translational modification) within proteins.

Protein Structure

http://www.sbg.bio.ic.ac.uk/~phyre2/html/page.cgi?id=index Phyre2 provides protein secondary and tertiary structural predictions based upon sequence homology. It also provides a prediction of intrinsically disordered regions in proteins.
http://www.proteinmodelportal.org ProteinModelPortal provides protein structural predictions based upon sequence homology.
http://pfam.xfam.org/ Provides predictions for functional domains within proteins.

Localisation (Subcellular & Tissue Distribution)

http://www.proteinatlas.org A large group dedicated to making multiple antibodies against every human protein. These antibodies are used to stain human tissues for that protein to measure it’s abundance/localisation/tissue specificity.
http://compartments.jensenlab.org/Search Aggregates different data sources with subcellular localisation data/predictions.
https://www.proteomicsdb.org/ Aggregates different data sources with protein abundance data across different human tissues and human cell lines.
https://www.peptracker.com/epd Provides a graphically rich interface to a variety of proteome-wide experiments in human cells, mouse cells/tissues and C. elegans nematodes. Various protein characteristics are measured including localisation, turnover rate etc..
http://prolocate.cabm.rutgers.edu/index.cgi Provides a graphically rich interface for protein localisation data in rat liver tissue.

Protein Post-translational Modifications

http://www.phosphosite.org Aggregates different data sources with protein post-translational modification data and publications.
https://scansite4.mit.edu/ Provides predictions for functional sites (protein binding or post-translational modification) within proteins.

Protein Sequence or DNA Sequence Conservation

http://asia.ensembl.org/index.html Provides useful tree structures of the evolutionary conservation of genes and data on gene variants (splicing and SNPs).
http://phylomedb.org Provides useful tree structures of the evolutionary conservation of proteins.
http://inparanoid.sbc.su.se Provides a comprehensive analysis of the evolutionary conservation of proteins.
https://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl Provides analysis of the evolutionary conservation of proteins with links to organism-specific databases for matching genes/proteins.
http://lifemap-ncbi.univ-lyon1.fr/ Interactive tree of life to map evolutionary relationships.
http://www.timetree.org/ Map conservation to geological time.

Human and Model Animal Phenotypes

http://broadcvdi.org OR http://www.type2diabetesgenetics.org OR http://www.cerebrovascularportal.org/ Provides information on the association of target gene SNPs with human phenotypes.
https://www.gwascentral.org OR https://www.ebi.ac.uk/gwas/ Provides information on the association of target gene SNPs with human phenotypes.
https://www.wormbase.org/ If conserved in C. elegans this resource provides access to all of the observed phenotypes of disruption of that gene’s function in a living animal. There are corresponding databases for other organisms such as fruit flies, mice, yeast etc…
http://www.mousephenotype.org/ If conserved in mice this resource provides access to all the observed phenotypes of disruption of that gene’s function in a living animal.

scRNA-Seq

Genomic Promoter Analysis

Larance Laboratory