What is MDdb
MDdb provides a Science Gateway as an effort to address the lack of a global standard, metadata definitions, tools, and platforms that implement and enforce them, to share, find, access, operate, reuse, or reproduce numerical simulation digital research objects (e.g., Molecular Dynamics) -from methodological and analytical pipelines to raw trajectory data- based on the Findability, Accessibility, Interoperability, and Reusability (FAIR) principles.

What is the benefit
MDdb allows for registration and retrieval of records, citation, and cross-referencing information (see an example). Each entry is assigned a unique identifier (F, A, for humans and machines). The ID resolves to a Study Infopage with tools to interpret the work’s rich metadata (I, R, for humans and machines) and numerical simulation results by interactive 3D visualization through HTMoL or MDsrv+NGL.

Where does the data come from
Research groups that produce scientific numerical simulations around the world are the main data source. All fields with a molecular interest, experts or not, are the direct users. Furthermore, education institutions at all levels also benefit from this initiative.

How does it work
MDdb organizes and hosts detailed information about computational simulations. All MDdb entries are managed on a web server (F, A), represented in human and machine-readable formats (e.g., text and HTML). The latter are machine-actionable using the metadata and API provided by MDdb. The metadata contains detailed information about provenance, protocols, relevant links for rich citation, and cross-references to well-known identifiers (e.g., wwPDB or UniProt) that conform to data standards in the chemical and structural biology domains (I, R). MDdb metadata is kept in the Resource Description Framework (RDF) representation, which explicitly types all records, leaving no ambiguity about what the data represents (R).