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386 lines
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Plaintext
386 lines
13 KiB
Plaintext
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STRIDE: Protein secondary structure assignment
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from atomic coordinates
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Dmitrij Frishman & Patrick Argos
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European Molecular Biology Laboratory
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Postfach 102209, Meyerhofstr. 1
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69012 Heidelberg
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Germany
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FRISHMAN@EMBL-HEIDELBERG.DE
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ARGOS@EMBL-HEIDELBERG.DE
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CONTENTS
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1. About the method
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2. Copyright notice
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3. Availability
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4. Installation
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5. Using STRIDE
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6. Output format
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7. Bug reports and user feedback
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8. References
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----------------------------------------------------------------------
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1. About the method
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STRIDE [1] is a program to recognize secondary structural elements in
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proteins from their atomic coordinates. It performs the same task as
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DSSP by Kabsch and Sander [2] but utilizes both hydrogen bond energy
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and mainchain dihedral angles rather than hydrogen bonds alone. It
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relies on database-derived recognition parameters with the
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crystallographers' secondary structure definitions as a standard-of-
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truth. Please see Frishman and Argos [1] for detailed description of
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the algorithm.
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2. Copyright notice
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
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BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
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ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
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CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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For calculation of the residue solvent accessible area the program NSC
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[3,4] is used and was kindly provided by Dr. F.Eisenhaber
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(EISENHABER@EMBL-HEIDELBERG.DE). Please direct to him all questions
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concerning specifically accessibility calculations.
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3. Availability
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Executables of STRIDE for several UNIX platforms, VAX/VMS, OpenVMS,
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Dos and Mac together with documentation and source code are available
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by anonymous FTP from ftp.ebi.ac.uk (directories
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/pub/software/unix/stride, /pub/software/dos/stride,
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/pub/software/vms/stride, /pub/software/mac/stride). We are willing to
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compile the program for other architectures if temporary access to
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them will be granted by an interested user.
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Data files with STRIDE secondary structure assignments for the current
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release of the PDB [5] databank are in the directory
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/pub/databases/stride of the same site. Atomic coordinate sets can be
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submitted for secondary structure assignment through electronic mail
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to stride@embl-heildelberg.de. A mail message containing HELP in the
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first line will be answered with appropriate instructions. See also
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WWW page http://www.embl-heidelberg.de/stride/stride_info.html.
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4. Installation
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For UNIX, DOS and Mac no installation is needed. Just download the
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executable corresponding to your platform, and you are all set. For
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VAX and OpenVMS you need only to link the executable with a logical
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name; for example:
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yourlogicalname:= $ $yourdiskname:[your.directory.name]stride.exe
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and then use yourlogicalname as the program name.
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5. Using STRIDE
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The only required parameter for STRIDE is the name of the file
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containing a set of atomic coordinates in PDB [5] format. By default
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STRIDE writes to standard output, i.e. your screen. On systems that
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allow to redirect output you can do so to create a disk file. Help is
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available if you just type STRIDE without parameters. The following
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options are accepted:
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-fFilename Write output to the file "Filename" rather than to
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stdout.
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-h Report hydrogen bonds. By default no hydrogen bond
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information is included in the output.
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-o Report secondary structure summary only.
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-rId1Id2.. Read only chains Id1, Id2 etc. of the PDB file *). All
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other chains will be ignored. By default all valid
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protein chains are read.
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-cId1Id2.. Process only chains Id1, Id2 ...etc *). Secondary
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structure assignment will be produced only for these
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chains, but other chains that are present will be taken
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into account while calculating residue accessible
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surface and detecting inter-chain hydrogen bonds and,
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possibly, interchain beta-sheets. By default all
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protein chains read are processed.
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-mFilename Generate a Molscript [6] file. Using the program
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Molscript by Per Craulis you can create a postscript
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picture of your structure. You can manually edit the
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Molscript file produced by STRIDE to achieve the
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desired orientation and to include additional details.
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-q[Filename] Generate sequence file in FASTA [7] format and die.
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Filename is optional. If no file name is specified,
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stdandard output is used.
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All options are case- and position-insensitive.
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Examples:
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1. Calculate secondary structure assignment for 1ACP including
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hydrogen bond information:
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stride 1acp.brk -h
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2. Calculate secondary structure assignment for 4RUB and write the
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output to the file 4rub.str
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stride 4rub.brk -f4rub.str
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3. Calculate secondary structure assignment for chain B of 4RUB.
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Ignore all other chains. Generate a Molscript file 4rub.mol.
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stride 4rub.brk -rb -m4rub.mol
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4. Calculate secondary structure assignment for chain C of 2GLS in
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the presence of chains A and B. Report secondary structure
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summary only.
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stride 2gls.brk -rabc -cc -o
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6. Output format
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STRIDE produces output that is easily readable both visually and with
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computer programs. The side effect of this conveniency is larger file
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size of individual STRIDE entries. Every record is 79 symbols long and
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has the following general format:
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Position Description
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1-3 Record code
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4-5 Not used
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6-73 Data
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74-75 Not used
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75-79 Four letter PDB code (if available)
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Below follows the description of each record type.
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Code Description and format of data
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REM Remarks and blank lines
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Format: free
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HDR Header. Protein name, date of file creation and PDB code
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Format: free
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CMP Compound.Full name of the molecule and identifying
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information
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Format: free
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SRC Species, organ, tissue, and mutant from which the molecule
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has been obtained
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Format: free
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AUT Names of the structure authors
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Format: free
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CHN File name and PDB chain identifier*).
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Format: File name beginning from position 6 followed
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by one space and one-letter chain identifier
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SEQ Amino acid sequence
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Format: 6-9 First residue PDB number
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11-60 Sequence
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62-65 Last residue PDB number
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STR Secondary structure summary
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Format: 11-60 Secondary structure assignment **)
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LOC Location of secondary structure elements
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Format: 6-17 Element name
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19-21 First residue name
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32-26 First residue PDB number
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28-28 First residue chain identifier
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36-38 Last residue name
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42-45 Last residue PDB number
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47-47 Last residue chain identifier
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ASG Detailed secondary structure assignment
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Format: 6-8 Residue name
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10-10 Protein chain identifier
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12-15 PDB residue number
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17-20 Ordinal residue number
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25-25 One letter secondary structure code **)
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27-39 Full secondary structure name
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43-49 Phi angle
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53-59 Psi angle
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65-69 Residue solvent accessible area
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DNR Donor residue
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Format: 6-8 Donor residue name
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10-10 Protein chain identifier
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12-15 PDB residue number
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17-20 Ordinal residue number
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26-28 Acceptor residue name
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30-30 Protein chain identifier
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32-35 PDB residue number
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37-40 Ordinal residue number
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42-45 N..0 distance
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47-52 N..O=C angle
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54-59 O..N-C angle
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61-66 Angle between the planes of donor
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complex and O..N-C
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68-73 angle between the planes of acceptor
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complex and N..O=C
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ACC Acceptor residue
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Format: 6-8 Acceptor residue name
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10-10 Protein chain identifier
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12-15 PDB residue number
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17-20 Ordinal residue number
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26-28 Donor residue name
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30-30 Protein chain identifier
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32-35 PDB residue number
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37-40 Ordinal residue number
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42-45 N..0 distance
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47-52 N..O=C angle
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54-59 O..N-C angle
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61-66 Angle between the planes of donor
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complex and O..N-C
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68-73 angle between the planes of acceptor
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complex and N..O=C
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HDR, CMP, SCR and AUT records are directly copied from the PDB file,
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if supplied by the authors. If only the secondary structure summary is
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requested, only CHN, SEQ, STR and LOC records will be output.
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Hydrogen bond information (records DNR and ACC) was made very
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redundant to facilitate human reading and will not be reported by
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default.
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*) IMPORTANT NOTE: if the protein chain identifier is ' ' (space), it
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will be substituted by '-' (dash) everywhere in the STRIDE output.
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The same is true for command line parameters involving chain
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identifiers where you have to specify '-' instead of ' '.
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**) One-letter secondary structure code is nearly the same as used in
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DSSP [2] (see Frishman and Argos [1] for details):
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H Alpha helix
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G 3-10 helix
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I PI-helix
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E Extended conformation
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B or b Isolated bridge
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T Turn
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C Coil (none of the above)
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For each record (data line) except those with codes REM and STR the
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number of fields is consistent and is readily suitable for processing
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with external tools, such as awk, perl, etc.
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7. Bug reports and user feedback
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Please send your suggestions, questions and bug reports to
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FRISHMAN@EMBL-HEIDELBERG.DE. Send your contact address to get
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information on updates and new features.
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8. References
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1. Frishman,D & Argos,P. (1995) Knowledge-based secondary structure
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assignment. Proteins: structure, function and genetics, 23,
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566-579.
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2. Kabsch,W. & Sander,C. (1983) Dictionary of protein secondary
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structure: pattern recognition of hydrogen-bonded and
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geometrical features. Biopolymers, 22: 2577-2637.
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3. Eisenhaber, F. and Argos, P. (1993) Improved strategy in
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analytic surface calculation for molecular systems: handling of
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singularities and computational efficiency. J. comput. Chem. 14,
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1272-1280.
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4. Eisenhaber, F., Lijnzaad, P., Argos, P., Sander, C., and Scharf,
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M. (1995) The double cubic lattice method: efficient approaches
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to numerical integration of surface area and volume and to dot
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surface contouring of molecular assemblies. J. comput. Chem. 16,
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273-284.
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5. Bernstein, F.C., Koetzle, T.F., Williams, G.J., Meyer, E.F.,
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Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T., and
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Tasumi, M. (1977) The protein data bank: a computer-based
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archival file for macromolecular structures. J. Mol. Biol. 112,
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535-542.
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6. Kraulis, P.J. (1991) MOLSCRIPT: a program to produce both
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detailed and schematic plots of protein structures. J. Appl.
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Cryst. 24, 946-950.
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7. Pearson, W.R. (1990) Rapid and sensitive sequence comparison
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with FASTP and FASTA. Methods. Enzymol. 183, 63-98.
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