source: tags/ms_r16q4/HELP_SOURCE/oldhelp/pfold.hlp

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UP      arb.hlp
UP      arb_ntree.hlp
UP      e4.hlp
UP      arb_edit4.hlp
UP      glossary.hlp

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# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}

#************* Title of helpfile !! and start of real strunk ********
TITLE           Protein Alignments

OCCURRENCE      ARB_EDIT4
                ARB_NTREE

DESCRIPTION

        Protein gene sequences and (predicted) protein primary structures (= amino
        acid sequences) as well as protein secondary structures can be stored in the
        ARB database and protein alignments can be created. Using import filters
        amino acid sequences and/or protein secondary structures can be imported from
        DSSP files. Refer to LINK{arb_import.hlp} and especially LINK{dssp_ift.hlp}
        for information on how this is done, please. Description of the DSSP code
        and format as well as an example file can be found there, too.
        
        Once a protein secondary structure is present as species in the database it
        can be converted to an SAI (see LINK{sp_sp_2_ext.hlp}) to use it as reference
        for comparing other protein secondary structures or amino acid sequences. SAIs
        can be created from the protein secondary structure information in a special
        field named 'sec_struct', too (see LINK{pfold_sai.hlp}). This is useful, if
        one has a protein secondary structure aligned along with the amino acid
        sequence.
        
        An approach for visualizing matches between protein structures has been
        incorporated in ARB. The match computation for sequences and secondary
        structures is based on the Chou-Fasman algorithm (see below) or adaptions
        to it and depends on the used match method. The match methods are described
        in detail in LINK{pfold_props.hlp} along with all other related settings that
        can be configured via the 'Properties' menu.

SECTION Overview of the Chou-Fasman Algorithm

        The Chou-Fasman algorithm is a statistical method for predicting a protein
        secondary structure from its amino acid sequence. It is based on the fact
        that certain amino acids tend to form or break alpha-helices ('H'),
        beta-sheets ('E') and beta-turns ('T'). The experimentally obtained
        Chou-Fasman parameters (former and breaker values) are used to predict the
        possible occurrence of the individual structure types which can then be
        merged to create a secondary structure summary. Further information on how
        this approach is used for protein structure match computation can be found
        in LINK{pfold_props.hlp} in section 'Description of Match Methods'.

SECTION REFERENCES

        [1] Chou-Fasman Algorithm
        
                Details on the Chou-Fasman algorithm can be found in the original
                paper: "Chou, P. and Fasman, G. (1978). Prediction of the secondary
                structure of proteins from their amino acid sequence. Advanced
                Enzymology, 47, 45-148.".

        [2] DSSP
        
                The DSSP program was developed to standardize secondary structure
                assignment. It assigns protein secondary structures to amino acid
                sequences from the amino acids' crystallographic atom coordinates
                as specified by protein entries in the Protein Data Bank (PDB). The
                program can be found on the web at
                "LINK{http://swift.cmbi.ru.nl/gv/dssp/}". Details on the algorithm
                can be found in "Kabsch, W. and Sander, C. (1983). Dictionary of
                protein secondary structure: pattern recognition of hydrogen-bonded
                and geometrical features. Biopolymers, 22 (12), 2577-2637.
                PMID: 6667333; UI: 84128824."

NOTES

        The used method for protein secondary structure prediction, i.e. the Chou-Faman
        algorithm, is fast which was the main reason for choosing it. Performance is
        important for a large number of sequences loaded in the editor. However, it
        is not very accurate and should only be used as rough estimation. Thus, the
        match computation can only give an approximate overview if a given amino acid
        sequence matches a certain secondary structure.

EXAMPLES        None

WARNINGS        Protein secondary structure in the field 'sec_struct' is not aligned
                automatically with the sequence (yet). It has to be aligned manually!

BUGS            The editor might be unstable and may crash if sequences are not formatted.