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PROTCOM: searchable database of protein complexes enhanced with domain-domain structures.

ABSTRACT: The database of protein complexes (PROTCOM) is a compilation of known 3D structures of protein-protein complexes enriched with artificially created domain-domain structures using the available entries in the Protein Data Bank. The domain-domain structures are generated by parsing single chain structures into loosely connected domains and are important features of the database. The database (http://www.ces.clemson.edu/compbio/protcom) could be used for benchmarking purposes of the docking and other algorithms for predicting 3D structures of protein-protein complexes. The database can be utilized as a template database in the homology or threading methods for modeling the 3D structures of unknown protein-protein complexes. PROTCOM provides the scientific community with an integrated set of tools for browsing, searching, visualizing and downloading a pool of protein complexes. The user is given the option to select a subset of entries using a combination of up to 10 different criteria. As on July 2006 the database contains 1770 entries, each of which consists of the known 3D structures and additional relevant information that can be displayed either in text-only or in visual mode.

SUBMITTER: Kundrotas PJ

PROVIDER: S-EPMC1635331 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundMedical school curricula strives to teach as much material as can be retained in a limited amount of time. A common "gold standard" resource used building curricula are medical objectives suggested by national societies. Unfortunately these objectives suffer from several functional limitations such as limited accessibility to society members, non-searchable formats (such as nested tables or pdf images), and inability to compare and search across societal objectives for redundancy or gaps. The shift towards integrated curriculums in medical school also highlights the need to access suggested content across classical discipline categories.Main bodyWe have codified recommendations from national societies in the United States for medical school objectives in a common tabular format and developed an open access database which can be searched across disciplines and societies. A front end website that allows for searching objectives by keyword while filtering on society or discipline was created. The objectives returned from the initial search can be subsearched by a second term. There is a large range in the format, age, breadth, quantity, and quality of objectives from different societies. Some unique disciplines have overlapping suggested content though most of the content does seem "binnable" by discipline. The choice of metadata for objectives from each given society was also very inconsistent.ConclusionA free and searchable database of medical content to deliver during medical school has been developed with over 13,000 objectives from 18 societies and 22 disciplines at http://data.medobjectives.marian.edu/ . The normalization of the different disciplines' objectives into a common database allows a platform to standardize objectives moving forward. Future work could include adding user accounts to access the database, submission of new objectives, voting up and down suggested objectives, and adding "answers" mapped to objectives. Keyword tagging could allow import of content (e.g. PowerPoints) and outputting of suggested objectives, which would also allow comparison of curriculum across medical schools.

Dataset Information

PROTCOM: searchable database of protein complexes enhanced with domain-domain structures.

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