About the Protein Folding Database

From Foldeomics Wiki

The last 10 years have witnessed a revolution in our understanding of the pathway and stability of protein folding. The recent flood of sequence data, rapid structure determination, and radical developments in experimental methods has created an explosion in the amount of experimental biophysical folding data. The growth of folding data is expected to continue into future years as structural genomics projects gain momentum. In order to address this we have created the Protein Folding Database (PFD), a relational database that collects thermodynamic and kinetic data for the folding of proteins into a searchable, structured repository

Using the web interface, a user can search for & retrieve a detailed spreadsheet-like list of results, which can then be ordered to allow quick visualisation of PFD data entries. Each entry contains information of the publication and a URL to the entry in NCBI PubMed literature database. Information on individual proteins relies heavily on the hierarchy used by the Structural Classification of Proteins database (SCOP): proteins belong to families, which in turn belong to a structural class (e.g., all alpha proteins). This was done to minimize redundancy in the database - all structural information for an entry can be retrieved via the SCOP link. SCOP and PDB provide an array of links to other databases (e.g. Entrez, Pfam, ASTRAL), as well as an array of tools that operate on the data (e.g., 3D visualization). Effective use of hyperlinks in search results pages allows useful browsing. For example, simple searching may retrieve results for several proteins. Examining any entry in more detail yields information on the protein structure, folding thermodynamics and kinetics, experimental methods, mutations (if any), publication(s) and annotations. Because the hierarchy is hyperlinked, browsing of entries for other proteins belonging to the same class or family is straightforward.

The latest version incorporates standards set out by the Foldeomics Consortium. The Foldeomics Consortium consists of a group of experimental protein folding investigators, initially spanning 18 laboratories in eight countries. The goal of our efforts is to set uniform standards for the experimental community and to compile a dataset of the folding properties of a large number of reversibly folding proteins that will aid ongoing efforts to understand the folding process. These efforts incorporate several guidelines set out by Maxwell et al (2005).

PFD runs on MySQL relational database server software (version 4.1.18), hosted by an Apple Dual 2 GHz G5/OS X Server (version 10.4.7) and Apache 1.3.33. The database consists of 38 tables. All web-based forms and query interfaces to the database were created using a multi-tier web site written in PHP 5.1.2. and PEAR database abstraction classes.

PFD was created by Mark Bate, Chris Betts, Kate F. Fulton and Ashley M. Buckle at the Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia. PFD was supported by the Victorian Bioinformatics Consortium and funded by the Australian Research Council. Kate Fulton is also an NHMRC Peter Doherty fellow.

We would also like to thank the following students (Diploma of Software Development at Swinburne University of Technology (TAFE Division), Lilydale Campus): Robert Tipping, John Derrick, Ben Brumm and Danny Brain.

The following people have also contributed to the project:
Glyn L. Devlin, Rachel A. Jodun, Steve Bottomley, Alan R. Fersht, Abdullah A Amin, Noel Faux and Khalid Mahmood

We are very grateful to the following people for initial discussions, valuable suggestions and enthusiasm:
Neil Ferguson, Christopher Johnson, Stefano Gianni, Ugo Mayor, Satoshi Sato.

We thank Ross Coppel, James Whisstock, and Christina Mitchell for financial support.

Please cite the following publication when referring to PFD:
Fulton KF, Devlin GL, Jodun RA, Silvestri L, Bottomley SP, Fersht AR, Buckle AM. (2005) PFD: a database for the investigation of protein folding kinetics and stability. Nucleic Acids Res. 33 Database Issue:D279-283.
Kate F. Fulton, Mark A. Bate, Noel G. Faux, Khalid Mahmood, Chris Betts and Ashley M. Buckle (2007) Protein Folding Database (PFD 2.0): an online environment for the International Foldeomics Consortium. Nucleic Acids Res. 33 Database Issue:D304-307.

Ashley M. Buckle October 2006

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