nearest neighbor approaches were developed to predict the folding stabilities of nucleic acid secondary structures ( 1 ) . these parameter sets utilize empirical rules , generally derived from optical melting experimental data , as the basis of the predictions . for rna , rules exist for predicting both free energy and enthalpy change of watson  crick helices , gu pairs and loops ( 25 ) . parameters for dna have also been assembled for predicting watson crick pair free energy and enthalpy change and free energy changes of loops ( 6,7 ) . these parameter sets are the basis of computer programs that predict low free energy secondary structures . such programs include mfold / unafold ( 8,9 ) , the vienna rna package ( 10 ) , rna structure ( 2 ) , rnasoft ( 11 ) and sfold ( 12 ) . additional approaches that use statistical learning of parameters for rna folding have also used the rules from the nearest neighbor methods and derived new parameter values ( 13,14 ) . nearest neighbor parameter sets include both a set of rules , called either equations or features , for predicting stability and a set of parameter values used by the equations ( 14 ) . for rna , separate rules exist for predicting stabilities of helices , hairpin loops , small internal loops , large internal loops , bulge loops , multibranch loops , exterior loops and pseudoknots . given the number of rules and constraints on the length of journal publications , it is difficult to assemble all the parameters in one publication and provide meaningful tutorials for using the parameters . this is a barrier to software development for novel algorithms that could take advantage of the parameters . for example , many software packages that use rna parameters still implement the set of parameters assembled in 1999 ( 4 ) , in spite of the fact the rna parameters were updated in 2004 ( 2 ) based on experimental results . the nearest neighbor database ( nndb ) is a web - based tool for assembling and archiving complete nearest neighbor sets , including rules and values . currently , the 1999 and 2004 sets of rna folding parameters are provided ( 25 ) . the nndb is built using a set of static html , specifically xhtml 1.0 transitional pages with a page hierarchy shown in figure 1 . text is encoded in unicode ( utf-8 ) to facilitate display of equations in pages with diverse browsers running on diverse operating systems . the top - level page provides access to a help page , available parameter sets and a page of references to rna optical melting experiments . additionally , links provide downloading of the whole database in either zip or gzipped tar format . the help page introduces the purpose of the database and defines basic terms , including the set of structural features defined by secondary structures . for example , figure 2 , from the help page , shows an rna secondary structure that illustrates the loop features covered by nearest neighbor parameter sets . the basic equations for utilizing the parameters to extrapolate folding free energy changes to temperatures other than 37c and to predict melting temperatures are also provided . this figure illustrates the page hierarchy by following the linked pages down through the 1999 parameters and down to the hairpin loop pages . note that there are five example calculations for hairpin loops to illustrate the separate sequence - dependent rules that are used depending on the specific loop . figure 2.an rna secondary structure illustrating the types of features included in nearest neighbor parameter sets . internal loops have nucleotides not in canonical pairs on each of two strands , but bulge loops have nucleotides not in canonical pairs on only one strand . formally , a pseudoknot occurs when there are at least two pairs , with indices i paired to j and i paired to j , that satisfy the condition i < i < j < j. the pseudoknot helix is often considered to be composed of the fewest pairs that need to be removed to relieve the pseudoknot ( 19 ) . in this structure , this figure illustrates the page hierarchy by following the linked pages down through the 1999 parameters and down to the hairpin loop pages . note that there are five example calculations for hairpin loops to illustrate the separate sequence - dependent rules that are used depending on the specific loop . an rna secondary structure illustrating the types of features included in nearest neighbor parameter sets . internal loops have nucleotides not in canonical pairs on each of two strands , but bulge loops have nucleotides not in canonical pairs on only one strand . formally , a pseudoknot occurs when there are at least two pairs , with indices i paired to j and i paired to j , that satisfy the condition i < i < j < j. the pseudoknot helix is often considered to be composed of the fewest pairs that need to be removed to relieve the pseudoknot ( 19 ) . in this structure , the tan nucleotides are in pairs that could be removed to relieve the pseudoknot . for each set of parameters , for example , the 1999 rna rules predict only folding free energy changes ( 4 ) , but the 2004 rules can be used to predict both folding free energy and enthalpy changes ( 2,5 ) . for each structural feature , a page defines the basic equations and provides links to parameter values ( in plain text and html ) , references and tutorial pages ( e.g. figure 3 ) . the number of tutorials varies from feature to feature ; the set of tutorials is designed to cover each type of rule that can be encountered in practice . crick helix parameters are covered with two tutorials , one for self - complementary and one for non - self - complementary strands . these two tutorials also demonstrate the difference in the calculation when there are terminal au base pairs , which receive a free energy and enthalpy change penalty ( 3 ) , because the self - complementary duplex example has two terminal au pairs and the non - self - complementary case has no terminal au pairs . this tutorial demonstrates the prediction of folding free energy change for a hairpin loop of six unpaired nucleotides using the 2004 parameters ( 2,3 ) . an example tutorial from the database . this tutorial demonstrates the prediction of folding free energy change for a hairpin loop of six unpaired nucleotides using the 2004 parameters ( 2,3 ) . individual pages above the level of value tables have top banner , a left navigation bar that allows the user to navigate back up the hierarchy to any level above and a bottom bar with the date of last editing . for pages edited after the database has gone online , previous versions of the page are available using this bottom content bar . to facilitate indexing by search engines , all pages have a descriptive title , including the set of parameters to which it belongs ( if applicable ) . the first release of the nndb contains the rna folding rules assembled in 1999 and 2004 ( 25 ) . these rules represent the most recent set of parameters and a prior set that is widely used in software packages . because folding rules are derived to work as a set , the two versions of rules and values should not be mixed and the website hierarchy reinforces this . it is anticipated , for example , that additional pages will be written to include nearest neighbors for dna folding ( 6,7 ) and for predicting rna pseudoknot stabilities ( 1518 ) . additionally , the values derived from the re - estimation of the values of the 1999 parameter set using the set of known rna secondary structures will also be included ( 14 ) . the nndb is designed to provide a convenient location for assembling parameter sets for predicting the stability of nucleic acid secondary structures . it is modular in design , which facilitates its future expansion to contain additional parameter sets . furthermore , the web format makes it feasible to provide extensive tutorials for utilizing the parameters , which is generally not possible in print . the creation of the nndb was supported by united states national institutes of health grants gm076485 to d.h.m . and gm22939 to d.h.t . funding for open access charge : united states national institutes of health .
the nearest neighbor database ( nndb , http://rna.urmc.rochester.edu/nndb ) is a web - based resource for disseminating parameter sets for predicting nucleic acid secondary structure stabilities . for each set of parameters , 
 the database includes the set of rules with descriptive text , sequence - dependent parameters in plain text and html , literature references to experiments and usage tutorials . 
 the initial release covers parameters for predicting rna folding free energy and enthalpy changes .