Protein Data Resources

The broad outline of biomedical knowledge conforms to the central dogma of molecular biology – DNA is transcribed into RNA that is translated into protein. In addition, the databases containing that knowledge must first gather the information resulting from research, and then present information through interpretations that enable further study and research. The encoded polypeptide sequences of proteins and the transcribed polynucleotide sequences of RNA are only the beginning of the story – we want to know how they are processed, how they interact and function, and how, finally, they are targeted for recycling. There are numerous resources devoted to describing proteins from their sequences, their three-dimensional structures, their functions, how they interact with each other and their context within the cell. Some resources are depositories of the results from experiments such as sequencing, mass spectrometry, X-ray crystallography, or immunofluorescence analysis. Others add annotations to describe protein features and functions from predictions or bring together orthogonal experimental results, often from the literature. Additionally, other resources present an infrastructure to organize and present collections of primary and derived data together. The major developments in molecular biology within the past 10 years have been the emergence of the large-scale omics technologies. They have greatly increased our knowledge of the molecular structures as they exist and function in the cell and the organism. This is reflected in the acquisition and organization of new knowledge within the bioinformatics database resources. Here, we describe in overview those resources.