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Paper text:
protein structure comparison ( psc ) has been a staple method for obtaining information about a protein when its 3d structure is determined experimentally or predicted computationally .
it is therefore not surprising that the development of new psc algorithms has been continuing for more than two decades with no sign of ceasing ( 16 ) .
these efforts are needed not only to meet new scientific challenges but also to benefit maximally from the large number of new structures now pouring in from structural genomics projects ( 7,8 ) . to these ends , a number of laboratories have created psc servers in recent years to provide information beyond the basic psc operations , including , e.g. those that do flexible alignment ( 9,10 ) , those that discover recurring substructures or motifs ( 11,12 ) , those that perform multiple structure alignment ( 13 ) and those that focus on fast structure feature extraction ( 1416 ) . here
we offer a new psc server with the functionality to report statistically significant alternative alignments ( 17,18 ) and structural permutations ( 19,20 ) at all levels of complexity .
our method , named opaas , which has been detailed elsewhere ( 21,22 ) , deduces the probabilities of aligning every possible pair of secondary structure elements ( sses ) between two protein structures prior to the search for a solution of their alignment .
this deduction allows the ready identification of most , though not all , statistically significant alignment solutions , many of which being distinct alternatives to the  optimal solution , the target of conventional psc operations . as we reported previously from a study of all - against - all database comparisons ( 22 ) , about half of the alternative alignments
moreover , many of the permuted alignments exhibited a permutation complexity higher than that of circular permutation , meaning that more than two separable regions of the protein structure could be aligned non - sequentially . to quantitatively measure the level of permutation complexity for all the alignments , we devised a permutation index ( pi ) as follows : 
 pi=(i=1nsi)2i=1nsi2 , 
 where si is the size ( number of aligned amino acid residues ) of the aligned region i and n is the total number of aligned regions .
a region is an independently , and , within the region itself , topologically aligned part of an alignment .
that is , within a region , all the aligned residues are ordered sequentially , which may or may not be interrupted by gaps , but these regions , if there are more than one , are aligned non - sequentially .
it follows that an alignment without any permutation will have just one region , and will have , by definition , a pi value of 1.0 . also by definition , a circular permutation , which involves swapping two regions in a non - topological alignment ( 19,20 ) , will receive a pi value > 1.0 but not > 2.0 .
pi hence furthermore let us know how much the sizes of the separately aligned regions differ .
for example , given two permuted protein pairs having pi 3.0 and 2.5 , respectively , we will know that they both have three aligned regions , but the sizes of the three regions are equal for the former and vary significantly for the latter .
both permuted and non - permuted alternative alignments are reported by the opaas server in a fashion that is easy for a non - specialist user to grasp the main significance of the comparison as one would with the 
this is aided by the server 's user - friendly interfaces described below , which use intuitive viewing directions , informative tables that can be sorted by different parameters , cascading information windows , and a structured user guide with examples .
at the portal of the opaas web server ( figure 1a ) lay two main structure comparison functions ,  1 against scop90 dataset and  2 chains alignment , and a help webpage for a structured opaas user guide , which can be viewed on - line ( ) as well as interactively in different contexts ( see below ) . the one - against - all on scop90 function is designed to find structural neighbors of a protein of interest in the structure classification of proteins ( scop ) ( 23 ) database .
one of the following three input options ( left panel in figure 1b and user guide 3.1.1 ) is available for the search : a structure domain already in scop90 ( scop version 1.55 , < 90% sequence identity non - redundant set ) , a structure in the current protein data bank ( pdb ; the server updates its local pdb weekly ) ( 24 ) with a specified chain ( pdb i d option ) , or a structure in pdb format uploaded by user ( user 's structure option ) .
all of the three inputs can be accompanied with optional parameter settings for customized output .
the parameters that could be changed from default include minimum rough z - score [ for the alignment prior to refinement ( 21 ) ] , minimum refined z - score , maximum root mean square deviation ( rmsd ) of c superposition between two aligned protein chains , minimum aligned sequence identity , maximum number of shown matches , and sorting options ( right panel in figure 1b and user guide 3.1.2 ) .
unlike the first input option , for which pre - computed results will be retrieved , the last two input options require entry of user 's e - mail address ( user guide 3.1.3 ) because the opaas server needs time for computation and will return the result via e - mail in , typically , minutes to hours , depending mainly on the stringency of the selected parameters . for the first input option , a table of matched results retrieved from a pre - computed database will be displayed directly on the web page ( figure 1c and user guide 3.2 ) . in this table ,
z - score , # a.a . aligned ( number of aligned amino acids ) , and
sol . is the number of alternative alignment solutions that satisfy the parameters specified by the user , and pi indicates the level of permutation complexity as described above .
user can sort the table by the field selected ( user guide 3.2.2 ) and download this table either as a plain text file or a comma separated values format file ( user guide 3.2.3 ) .
user also can click on the matched entry to view details of each alignment solution , which will have exactly the same output as that from using the function of  2 chains alignment ( user guide 3.2.4 ; see below ) . for the output of the last two input options , an e - mail of search result with the subject title 
opaas result will be sent back to the e - mail address supplied ( user guide 3.3 ) .
the e - mail contains a table of search result like that of the first input option described above , but to interactively view details of individual alignment solution , the second function , described below , needs to be separately invoked . for the function of  2 chains alignment ( figure 1d and user guide 4.1 ) , the structures of the two protein chains could either be selected from pdb ( i.e. entering pdb i d ) or uploaded by user in pdb format .
display of the comparison results , which can be expected to follow immediately upon submission of the request , is split into three frames to show
 basic information of the comparison ,  information of each solution , and  detail alignment of selected region ( figure 1e and user guide 4.2 ) .
in the frame of  basic information of the comparison , one of two tables gives some basic information about the two chains compared : size ( number of amino acid residues ) , and number of sse ( user guide 4.2.1 ) .
user can click a hyperlink on the name of the two chains placed above the table to learn more about the compared proteins from the pdb website ( user guide 4.2.2 ) .
the other table shows information of all the solutions ( both the  optimal and alternative alignments , if any ) of this comparison including # a.a .
aligned ( number of aligned residues ) , rmsd , refined z - score , pi and region ( number of permutedly aligned regions ) .
clicking on the solution number shows details of that solution in another two frames ( user guide 4.2.3 ) .
the frame of  information of each solution shows the alignment of the selected solution graphically ( user guide 4.2.4 ) , both in a schematic representation and in a 3d superposition supported by chime plug - in ( user guide 4.2.5 ) .
a file containing cartesian coordinates of this alignment solution in standard pdb format can be exported .
different colors of the boxes in the diagram of the schematic representation , as well as of the traces in the 3d superposition , refer to different aligned regions .
clicking on the region box will show  detail alignment of the selected region in the third frame .
the sequence alignment of this region can also be downloaded in mfa ( multi - fasta alignment ) format by clicking 
the one - against - all on scop90 function is designed to find structural neighbors of a protein of interest in the structure classification of proteins ( scop ) ( 23 ) database .
one of the following three input options ( left panel in figure 1b and user guide 3.1.1 ) is available for the search : a structure domain already in scop90 ( scop version 1.55 , < 90% sequence identity non - redundant set ) , a structure in the current protein data bank ( pdb ; the server updates its local pdb weekly ) ( 24 ) with a specified chain ( pdb i d option ) , or a structure in pdb format uploaded by user ( user 's structure option ) .
all of the three inputs can be accompanied with optional parameter settings for customized output .
the parameters that could be changed from default include minimum rough z - score [ for the alignment prior to refinement ( 21 ) ] , minimum refined z - score , maximum root mean square deviation ( rmsd ) of c superposition between two aligned protein chains , minimum aligned sequence identity , maximum number of shown matches , and sorting options ( right panel in figure 1b and user guide 3.1.2 ) .
unlike the first input option , for which pre - computed results will be retrieved , the last two input options require entry of user 's e - mail address ( user guide 3.1.3 ) because the opaas server needs time for computation and will return the result via e - mail in , typically , minutes to hours , depending mainly on the stringency of the selected parameters . for the first input option , a table of matched results retrieved from a pre - computed database will be displayed directly on the web page ( figure 1c and user guide 3.2 ) . in this table ,
z - score , # a.a . aligned ( number of aligned amino acids ) , and
sol . is the number of alternative alignment solutions that satisfy the parameters specified by the user , and pi indicates the level of permutation complexity as described above .
user can sort the table by the field selected ( user guide 3.2.2 ) and download this table either as a plain text file or a comma separated values format file ( user guide 3.2.3 ) .
user also can click on the matched entry to view details of each alignment solution , which will have exactly the same output as that from using the function of  2 chains alignment ( user guide 3.2.4 ; see below ) . for the output of the last two input options , an e - mail of search result with the subject title 
opaas result will be sent back to the e - mail address supplied ( user guide 3.3 ) .
the e - mail contains a table of search result like that of the first input option described above , but to interactively view details of individual alignment solution , the second function , described below , needs to be separately invoked .
for the function of  2 chains alignment ( figure 1d and user guide 4.1 ) , the structures of the two protein chains could either be selected from pdb ( i.e. entering pdb i d ) or uploaded by user in pdb format .
display of the comparison results , which can be expected to follow immediately upon submission of the request , is split into three frames to show  basic information of the comparison ,  information of each solution , and  detail alignment of selected region ( figure 1e and user
basic information of the comparison , one of two tables gives some basic information about the two chains compared : size ( number of amino acid residues ) , and number of sse ( user guide 4.2.1 ) .
user can click a hyperlink on the name of the two chains placed above the table to learn more about the compared proteins from the pdb website ( user guide 4.2.2 ) .
the other table shows information of all the solutions ( both the  optimal and alternative alignments , if any ) of this comparison including # a.a .
aligned ( number of aligned residues ) , rmsd , refined z - score , pi and region ( number of permutedly aligned regions ) .
clicking on the solution number shows details of that solution in another two frames ( user guide 4.2.3 ) .
the frame of  information of each solution shows the alignment of the selected solution graphically ( user guide 4.2.4 ) , both in a schematic representation and in a 3d superposition supported by chime plug - in ( user guide 4.2.5 ) .
a file containing cartesian coordinates of this alignment solution in standard pdb format can be exported .
different colors of the boxes in the diagram of the schematic representation , as well as of the traces in the 3d superposition , refer to different aligned regions .
clicking on the region box will show  detail alignment of the selected region in the third frame .
the sequence alignment of this region can also be downloaded in mfa ( multi - fasta alignment ) format by clicking 
the best way to compare two protein structures often depends on the question being asked ( 6 ) , so having a server like opaas that can simultaneously analyze solutions beyond the 
although most of the published psc algorithms can be modified to offer similar capability , to our knowledge , only two psc servers give user the option to see alternative alignments : prosup ( 25 ) and sarf2 ( 26 ) , but prosup is limited to topological alignments and neither offers one - against - all database searching service .
moreover , with an intuitive hierarchical layout of the comparison results and optional parameter settings to view most significant alignments ( e.g. with similarity p - value set at 10 , a typical comparison usually resulted in < 5 such solutions ) , an informative summary that could lead to unexpected insight from unexpected alternative alignments is effectively produced .
the main limitation of opaas , at its current version , arose from a compromise to trade for computational efficiency , which dictates that a structure must possess at least three sses to be compared ( 21,22 ) ; elimination of this limitation is in progress .
significantly , our server allows database search with an efficiency comparable that of the popular ce server ( 27 ) , despite ours being run on a personal computer ( pentium iv ) and being asked to find alternative alignments .
the source code of opaas is also available at the server for free download for standalone computations and for incorporation of structure database other than scop .
( b ) the input page for the function of one - against - all search in the scop90 dataset .
three different input preferences and optional parameter settings are allowed in the left and right panel , respectively .
( c ) this table of matched results is retrieved from a database containing pre - computed all - against - all comparison results , which is available only with the one - against - all function .
the information of all alignment solutions (  optimal and alternatives ) is hierarchically laid out in three frames .
the large number of experimentally determined protein 3d structures is a rich resource for studying protein function and evolution , and protein structure comparison ( psc ) is a key method for such studies . 
 when comparing two protein structures , almost all currently available psc servers report a single and sequential ( i.e. topological ) alignment , whereas the existence of good alternative alignments , including those involving permutations ( i.e. non - sequential or non - topological alignments ) , is well known . 
 we have recently developed a novel psc method that can detect alternative alignments of statistical significance ( alignment similarity p - value < 105 ) , including structural permutations at all levels of complexity . 
 opaas , the server of this psc method freely accessible at our website ( ) , provides an easy - to - read hierarchical layout of output to display detailed information on all of the significant alternative alignments detected . 
 because these alternative alignments can offer a more complete picture on the structural , evolutionary and functional relationship between two proteins , opaas can be used in structural bioinformatics research to gain additional insight that is not readily provided by existing psc servers .