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POSA terms

POSA: Partial Order Structure Alignment
POA: Partial Order Alignment
POG: Partial Order Graph

POSA alignment output

POSA was developed to generate partial order alignments, which means that the output alignments are partial order graphs. So NO alignments in the typical column-row format will be provided.
POSA server provides two ways for displaying the partial order alignments; one can browse the alignment through our iterative webpage, or download the alignment text file.

How to read POA text file

POSA generates partial order alignments, which means we cannot provide the typical column-row alignments in whatever formats. Instead we provide TWO kinds of alignment output that might be useful for some users.
Here we use the POSA result of 3 calmodulin-like proteins to demonstrate. This page provides links to the two alignment outputs shown below.
(1) Partial Order Graph (POG) along with amino acids
This file (show me the demonstration file) records the list of proteins between <PRO>...</PRO>: d1ncx__ (index = 0), d2sas__ (index = 1) and d1jfja_ (index = 2).

Between <NODE> and </NODE>, each line represents a node in the POG, recording residues aligned at this node. For examples,
"0 0 0 A" records node 0 (note: all indexes are from 0), meaning residue 0 (residues are indexed starting from 0 regardless the original index in the PDB file) of protein 0 (i.e., d1ncx__), whose amino acid is A;
"20 0 20 E 2 0 M 1 8 K" records node 20, which represents an aligned position common to all 3 input structures (i.e., protein 0 residue 20 E, protein 2 residue 0 M and protein 1 residue 8 K are aligned at this node).
Between <EDGE> and </EDGE>, each line records an edge connecting two nodes; e.g., "0 0 1" records edge 0 connecting node 0 and node 1.
Between <CORE> and </CORE>: parameters about the common core for the input structures. For example:
<CORE>0 3 132 2.80 1 2.32</CORE> Length or size of the POG is enclosed in the <LEN> tag. For example:
<LEN>201 208</LEN> Users may prepare alignments they desire by extracting alignment information from this file.

(2) Alignment of amino acids

This file (show me the demonstration file) only explicitly lists the residues of aligned regions of at least 5-residues long shared by all input structures (but not aligned positions of a subset of the input structures), while only shows the lengths of the other spanning regions between {}.

in the file, the first line shows that there are 6 such aligned regions, labeled as S1 - S6 (same as in the simplified POSA graph).
The second line "d1ncx__ {20}EFKAAFDM{0}FDADGGGDIST{1}.." shows residues 21-28 of 1ncx__ (EFKAAFDM), 29-39 (FDADGGGDIST) and so on.

PDB inputs in a tar/zip file

POSA server accepts structures (in PDB format) packed in either a tar (gzipped or not) or a zip file. Be sure to only pack (a) clean PDB files (e.g., use a filtered PDB file that only contains a specific chain you want to use, instead of the original PDB file with multiple chains); and (b) files in current directory (instead of files in a subdirectory or mixed).

E.g., you have three structures, AAAA.pdb, BBBB.pdb and CCCC.pdb in current directory; you can archive these pdbs in three ways that POSA server can recognize.

> tar cvf pdb.tar AAAA.pdb BBBB.pdb CCCC.pdb
> tar zcvf pdb.tar.gz AAAA.pdb BBBB.pdb CCCC.pdb
> zip pdb.zip AAAA.pdb BBBB.pdb CCCC.pdb

PDB inputs with user-defined constrains

You can provide the PDB inputs with user-defined constrains either in text area provided in the POSA input page or you can upload a text file.

Please use the following example to undertand the text format of the PDB inputs with user-defined constrains:

#PDB    Chain   Segments        Reference    OtherChains
1a9n    B       NA      No      Q
1urn    A       11-16,40-46,55-60,76-86 Yes     P
2err    A       NA      No      B
1yty    A       NA      No      C
2kg1    A       NA      No      B
#PDBChainSegmentsReferenceOtherChains
1a9nBNANoQ
1urnA11-16,40-46,55-60,76-86YesP
2errANANoB
1ytyANANoC
2kg1ANANoB


ColumnDescription
PDBInitial protein structures in PDB file format or given by PDB codes. Required
A PDB file of column1.pdb should be given or will be downloaded from PDB’s site
ChainChain Id from column1.pdb that will be used for structure alignment. Required
SegmentsSegments defined by “resSeq-reqSeq” separated by comma, where "resSeq" is the residue sequence number field(column 23-26) in ATOM line.
Optional. Default=“NA”
It defines which Segments from the chain in column2 that will be used for structure alignment.
When absent, the whole chain will be used
ReferenceYes/No; Optional; default=“No”
Is this structure used as the reference, which means, all other structures will be aligned to this structure to result in the
multiple structure alignment. Only one reference is allowed if present and at this case, rigid pairwise structure alignment method will be used. Otherwise, POSA structure alignment method will be used.
OtherChainsChain Ids separated by comma.
Optional. Default=“NA”. When absent, then full chain in Column-2 will be used.
Are there any other chain(s) be included in the final multiple structure alignment for display purpose only. These chains are not used when calculating structure alignment but are added in the post process for users to view where these molecules are located in the multiple structure alignment.
Comment Line: start with "#"
Columns use spaces or tabs (default) as delimiters
There is no space in each cell content
If a cell is empty, please use "na" or "NA" as a placeholder.

How to visualize superimposed 3D structures

Multiple superimposed structures can be visualized iteratively on our website. Currently POSA supports only Jmol to display protein structures. In order to run Jmol, please make sure that Java is installed in your system and Java Applet Plug-in and Javascript are enabled in your web browser.