understanding the rules that govern protein folding is one of the great challenges of molecular biology .
studies of protein folding , combining experiment and simulation , have led to a solid understanding of the physical process of folding and the forces that stabilize proteins .
the last 10 years have witnessed a revolution in our understanding of the pathway and stability of protein folding ( 1 ) .
the sustained growth of folding studies is fuelled by the availability of new sequences , rapid structure determination and radical developments in experimental methods .
furthermore , recent successes in folding simulations have improved our understanding of the protein folding process at atomic resolution ( 2 ) , providing further avenues for experimental investigation .
analysis of the folding mechanisms and pathways of proteins within homologous families has propelled protein folding into the post - genomic era ( 3 ) . traditionally , kinetic and thermodynamic data are collected and analysed on an individual protein basis , and is published in an unstructured fashion , despite the best efforts to tabulate it .
clearly , this presents an enormous challenge for data analysis , even simple searching for trends requires exhaustive manual inspection of the literature . with the exception of protherm [ thermodynamic database for proteins and mutants ( 4 ) ] , the vast majority of web - accessible databases focus on sequences and structures .
there are currently no tools that bring together both kinetic and thermodynamic folding data for proteins and mutants .
a comparison of the folding properties for more than 50 proteins represents the most comprehensive compilation of folding data to date ( 5 ) .
this painstaking analysis uncovered some general trends but also highlighted the great diversity in folding behaviour .
the speed at which a protein folds and the pathway it takes are dictated by its structural and energetic characteristics .
recent work suggests that the fundamental physics underlying folding may be relatively simple : the mechanism of folding appears to be dictated by the low - resolution features ( or topology ) of the folded protein structure ( 6 ) .
topology can be described by the parameter contact order , which is defined as the average sequence separation between contacting residues in the 3d structure .
proteins having a low contact order , e.g. -helical bundles , fold faster than those with a high contact order , e.g. -sandwiches ( 6 ) .
topology has been found to be the overriding determinant of folding rate for a wide range of proteins ( 69 ) .
however , studies on the topologically similar members of the immunoglobulin family have shown that they fold with rate constants which correlate better with stability ( 10 ) .
studies on horse and yeast cytochrome c also suggest that stability is an important factor ( 11 ) .
furthermore , protein engineering studies show that mutations which do not affect the contact order can change the folding rate by many orders of magnitude ( 5 ) .
thus , in many cases , factors other than topology must also be significant . the last six years have witnessed a huge increase in the number of proteins being studied , and is set to grow further as structural genomics projects gain momentum . in order to exploit this wealth of data so that data mining efforts may uncover further relationships between folding behaviour and structural character ,
indeed , recent benchmarking of predicted folding rates ( 12 ) , together with comparisons of the folding behaviour of two- and three - state folding proteins ( 13 ) , emphasizes the need for a centralized database . in order to address this issue , here
, we describe the design and implementation of a relational database for protein folding , protein folding database ( pfd ) .
a user - friendly web interface to the database allows querying using many parameters , as well as retrieval and presentation of data .
the database will have three distinct roles : ( i ) data repository : new data can be rapidly deposited , validated and made available to the folding community and wider scientific arena ; ( ii ) experimental resource , the database will be of use to the biophysicist seeking to compare new folding data with the current dataset for similar proteins , bypassing the relatively slow and inefficient examination of the literature . the database will play a useful role in the design of folding experiments , e.g. both as a guide in the design of experimental methodology and in the selection of proteins belonging to homologous families ; and ( iii ) theoretical resource , all experimental folding data will be at the disposal of theoreticians , strengthening the emerging conspiracy between experiment and simulation .
our approach is to create a database that captures as much as possible of the relevant information important for a folding experiment : kinetic rates of folding and unfolding ; equilibrium free energies ; experimental methods such as spectroscopic technique ( probe ) and method of perturbation ( e.g. denaturant ) , and instrument details ; publication information ; protein details , such as fold , structural class , biological function and mutation information .
pfd was created using open - source mysql relational database server software , version 4.0.16 ( www.mysql.com ) , running on an apple dual 2.0 ghz g5/os x server ( version 10.3.4 ) .
a web - based query interface to the database was created using the java programming language and apple webobjects software ( version 5.2.2 ) and the xcode development environment ( figure 1 ) .
the essence of our approach is to allow a diverse collection of folding data to be searched via multiple parameters , and the results presented in a structured fashion .
typical queries that can be formulated are  compare the folding behaviour of monomeric -helical proteins? ; and  which beta proteins larger than 60 residues have folding rates greater than 10 s?. the web interface allows a detailed , spreadsheet - like list of results allowing quick visualization of general trends in data ( figure 2 ) . the results of a search can be sorted on any heading , which is useful , e.g. when inspecting the variability of folding rates among proteins within a family .
each entry also contains information of the publication and a url to the entry in ncbi pubmed literature database .
annotation of proteins exploits the hierarchy used by the structural classification of proteins database [ scop ( 14 ) ] : proteins belong to families , which in turn belong to a structural class ( e.g. all alpha proteins ) .
this was performed to minimize redundancy in the database so that all structural information for an entry can be retrieved via the scop link .
scop and pdb provide an array of links to other databases ( such as entrez , pfam and astral ) , as well as an array of tools that operate on the data ( e.g. 3d visualization ) .
the hierarchical classification of structural class / family / protein allows convenient browsing ( akin to browsing proteins belonging to a particular fold in scop ) : folding data for proteins are grouped under their fold or structural class , which may prove convenient when examining the folding behaviour of proteins within a family .
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 ( figure 3 ) .
the power of the relational database approach allows us to visualize folding data in a novel way .
availability and submissions : pfd is freely available at http://pfd.med.monash.edu.au . submissions and enquiries should be emailed to ashley.buckle@med.monash.edu.au .
the constructed database and web - based query interfaces have demonstrated the applicability and usefulness of the database design .
questions indicates that its design accurately reflects the organization of data in a real folding experiment .
future work will focus on the following areas : 
 functional annotation : an analysis of folding data must take into account the biological function of the protein .
any trends uncovered must also be considered in the context of function . to enable these entries
will be linked to the gene ontology database ( 15 ) , which annotates database entries on molecular function , biological process and cellular location.data exchange : how will other databases be able to use data from the folding database ?
this is a serious challenge because of the vast heterogeneity in database standards and data structure .
this can be addressed by making folding data available using extensible markup language ( xml ) .
xml provides the capability of representing protein data in a single , standardized data structure that is easily transmitted over a network .
this will require the construction of a specification language for protein folding data that will allow for portable , system - independent , machine - parsable and human - readable representation of essential features of protein folding .
all folding data can then be made available in xml format.data visualization : as the dataset grows , visualization of text becomes cumbersome .
this will require the development of graphical representations of the data , such as chevron plots .
in particular , graphical methods allowing the visualization of relationships between structural parameters , such as contact order and folding kinetics , will prove very useful.data deposition and validation : it is vital that new folding data is deposited in the same timeframe as publication ( as is the case of the pdb ) .
this means that the data becomes readily available to the community and amenable to analysis .
this can be achieved using a forms - based system that will allow data to be deposited , via a web - browser , directly by the originator of the data , again in an analogous manner to the pdb .
validation logic can also be built into the deposition process , providing both a useful service to the depositor as well as an indication on data quality to users .
the latter two aims are particularly important for database functionality and growth , respectively , and will be given priority .
this approach will allow us to achieve a high degree of uniformity in the structure of folding data , which will benefit experimentalists in data acquisition and handling .
functional annotation : an analysis of folding data must take into account the biological function of the protein .
any trends uncovered must also be considered in the context of function . to enable these entries
will be linked to the gene ontology database ( 15 ) , which annotates database entries on molecular function , biological process and cellular location .
data exchange : how will other databases be able to use data from the folding database ?
this is a serious challenge because of the vast heterogeneity in database standards and data structure .
this can be addressed by making folding data available using extensible markup language ( xml ) .
xml provides the capability of representing protein data in a single , standardized data structure that is easily transmitted over a network .
this will require the construction of a specification language for protein folding data that will allow for portable , system - independent , machine - parsable and human - readable representation of essential features of protein folding .
this will require the development of graphical representations of the data , such as chevron plots .
in particular , graphical methods allowing the visualization of relationships between structural parameters , such as contact order and folding kinetics , will prove very useful .
data deposition and validation : it is vital that new folding data is deposited in the same timeframe as publication ( as is the case of the pdb ) .
this means that the data becomes readily available to the community and amenable to analysis .
this can be achieved using a forms - based system that will allow data to be deposited , via a web - browser , directly by the originator of the data , again in an analogous manner to the pdb .
validation logic can also be built into the deposition process , providing both a useful service to the depositor as well as an indication on data quality to users .
the latter two aims are particularly important for database functionality and growth , respectively , and will be given priority .
this approach will allow us to achieve a high degree of uniformity in the structure of folding data , which will benefit experimentalists in data acquisition and handling .
we thank christina mitchell for financial support , and james whisstock and ross coppel for continuing support .
 we have developed a new database that collects all protein folding data into a single , easily accessible public resource . 
 the protein folding database ( pfd ) contains annotated structural , methodological , kinetic and thermodynamic data for more than 50 proteins , from 39 families . 
 a user - friendly web interface has been developed that allows powerful searching , browsing and information retrieval , whilst providing links to other protein databases . 
 the database structure allows visualization of folding data in a useful and novel way , with a long - term aim of facilitating data mining and bioinformatics approaches . 
 pfd can be accessed freely at http://pfd.med.monash.edu.au . 
INTRODUCTION
PFD DESCRIPTION
USE OF PFD IN FOLDING RESEARCH
CONCLUSIONS AND FUTURE DIRECTIONS
ACKNOWLEDGEMENTS