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| STRIDE: Protein secondary structure assignment |
| from atomic coordinates |
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| Dmitrij Frishman & Patrick Argos |
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| European Molecular Biology Laboratory |
| Postfach 102209, Meyerhofstr. 1 |
| 69012 Heidelberg |
| Germany |
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| FRISHMAN@EMBL-HEIDELBERG.DE |
| 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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| 1. About the method |
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| STRIDE [1] is a program to recognize secondary structural elements in |
| proteins from their atomic coordinates. It performs the same task as |
| DSSP by Kabsch and Sander [2] but utilizes both hydrogen bond energy |
| and mainchain dihedral angles rather than hydrogen bonds alone. It |
| relies on database-derived recognition parameters with the |
| crystallographers' secondary structure definitions as a standard-of- |
| truth. Please see Frishman and Argos [1] for detailed description of |
| the algorithm. |
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| 2. Copyright notice |
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| All rights reserved, whether the whole or part of the program is |
| concerned. Permission to use, copy, and modify this software and its |
| documentation is granted for academic use, provided that: |
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| i. this copyright notice appears in all copies of the software and |
| related documentation; |
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| ii. the reference given below (Frishman and Argos, 1995) must be |
| cited in any publication of scientific results based in part or |
| completely on the use of the program; |
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| iii. bugs will be reported to the authors. |
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| The use of the software in commercial activities is not allowed |
| without a prior written commercial license agreement. |
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| WARNING: STRIDE is provided "as-is" and without warranty of any kind, |
| express, implied or otherwise, including without limitation any |
| warranty of merchantability or fitness for a particular purpose. In no |
| event will the authors be liable for any special, incidental, indirect |
| or consequential damages of any kind, or any damages whatsoever |
| resulting from loss of data or profits, whether or not advised of the |
| possibility of damage, and on any theory of liability, arising out of |
| or in connection with the use or performance of this software. |
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| For calculation of the residue solvent accessible area the program NSC |
| [3,4] is used and was kindly provided by Dr. F.Eisenhaber |
| (EISENHABER@EMBL-HEIDELBERG.DE). Please direct to him all questions |
| concerning specifically accessibility calculations. |
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| 3. Availability |
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| Executables of STRIDE for several UNIX platforms, VAX/VMS, OpenVMS, |
| Dos and Mac together with documentation and source code are available |
| by anonymous FTP from ftp.ebi.ac.uk (directories |
| /pub/software/unix/stride, /pub/software/dos/stride, |
| /pub/software/vms/stride, /pub/software/mac/stride). We are willing to |
| compile the program for other architectures if temporary access to |
| them will be granted by an interested user. |
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| Data files with STRIDE secondary structure assignments for the current |
| release of the PDB [5] databank are in the directory |
| /pub/databases/stride of the same site. Atomic coordinate sets can be |
| submitted for secondary structure assignment through electronic mail |
| to stride@embl-heildelberg.de. A mail message containing HELP in the |
| first line will be answered with appropriate instructions. See also |
| 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 |
| executable corresponding to your platform, and you are all set. For |
| VAX and OpenVMS you need only to link the executable with a logical |
| 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 |
| containing a set of atomic coordinates in PDB [5] format. By default |
| STRIDE writes to standard output, i.e. your screen. On systems that |
| allow to redirect output you can do so to create a disk file. Help is |
| available if you just type STRIDE without parameters. The following |
| options are accepted: |
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| -fFilename Write output to the file "Filename" rather than to |
| stdout. |
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| -h Report hydrogen bonds. By default no hydrogen bond |
| 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 |
| other chains will be ignored. By default all valid |
| protein chains are read. |
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| -cId1Id2.. Process only chains Id1, Id2 ...etc *). Secondary |
| structure assignment will be produced only for these |
| chains, but other chains that are present will be taken |
| into account while calculating residue accessible |
| surface and detecting inter-chain hydrogen bonds and, |
| possibly, interchain beta-sheets. By default all |
| protein chains read are processed. |
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| -mFilename Generate a Molscript [6] file. Using the program |
| Molscript by Per Craulis you can create a postscript |
| picture of your structure. You can manually edit the |
| Molscript file produced by STRIDE to achieve the |
| desired orientation and to include additional details. |
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| -q[Filename] Generate sequence file in FASTA [7] format and die. |
| Filename is optional. If no file name is specified, |
| 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 |
| 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 |
| 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. |
| 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 |
| the presence of chains A and B. Report secondary structure |
| 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 |
| computer programs. The side effect of this conveniency is larger file |
| size of individual STRIDE entries. Every record is 79 symbols long and |
| has the following general format: |
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| Position Description |
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| 1-3 Record code |
| 4-5 Not used |
| 6-73 Data |
| 74-75 Not used |
| 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 |
| information |
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| Format: free |
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| SRC Species, organ, tissue, and mutant from which the molecule |
| 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 |
| 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 |
| 11-60 Sequence |
| 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 |
| 19-21 First residue name |
| 32-26 First residue PDB number |
| 28-28 First residue chain identifier |
| 36-38 Last residue name |
| 42-45 Last residue PDB number |
| 47-47 Last residue chain identifier |
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| ASG Detailed secondary structure assignment |
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| Format: 6-8 Residue name |
| 10-10 Protein chain identifier |
| 12-15 PDB residue number |
| 17-20 Ordinal residue number |
| 25-25 One letter secondary structure code **) |
| 27-39 Full secondary structure name |
| 43-49 Phi angle |
| 53-59 Psi angle |
| 65-69 Residue solvent accessible area |
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| DNR Donor residue |
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| Format: 6-8 Donor residue name |
| 10-10 Protein chain identifier |
| 12-15 PDB residue number |
| 17-20 Ordinal residue number |
| 26-28 Acceptor residue name |
| 30-30 Protein chain identifier |
| 32-35 PDB residue number |
| 37-40 Ordinal residue number |
| 42-45 N..0 distance |
| 47-52 N..O=C angle |
| 54-59 O..N-C angle |
| 61-66 Angle between the planes of donor |
| complex and O..N-C |
| 68-73 angle between the planes of acceptor |
| complex and N..O=C |
| ACC Acceptor residue |
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| Format: 6-8 Acceptor residue name |
| 10-10 Protein chain identifier |
| 12-15 PDB residue number |
| 17-20 Ordinal residue number |
| 26-28 Donor residue name |
| 30-30 Protein chain identifier |
| 32-35 PDB residue number |
| 37-40 Ordinal residue number |
| 42-45 N..0 distance |
| 47-52 N..O=C angle |
| 54-59 O..N-C angle |
| 61-66 Angle between the planes of donor |
| complex and O..N-C |
| 68-73 angle between the planes of acceptor |
| complex and N..O=C |
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| HDR, CMP, SCR and AUT records are directly copied from the PDB file, |
| if supplied by the authors. If only the secondary structure summary is |
| requested, only CHN, SEQ, STR and LOC records will be output. |
| Hydrogen bond information (records DNR and ACC) was made very |
| redundant to facilitate human reading and will not be reported by |
| default. |
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| *) IMPORTANT NOTE: if the protein chain identifier is ' ' (space), it |
| will be substituted by '-' (dash) everywhere in the STRIDE output. |
| The same is true for command line parameters involving chain |
| identifiers where you have to specify '-' instead of ' '. |
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| **) One-letter secondary structure code is nearly the same as used in |
| DSSP [2] (see Frishman and Argos [1] for details): |
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| H Alpha helix |
| G 3-10 helix |
| I PI-helix |
| E Extended conformation |
| B or b Isolated bridge |
| T Turn |
| C Coil (none of the above) |
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| For each record (data line) except those with codes REM and STR the |
| number of fields is consistent and is readily suitable for processing |
| 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 |
| FRISHMAN@EMBL-HEIDELBERG.DE. Send your contact address to get |
| 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 |
| assignment. Proteins: structure, function and genetics, 23, |
| 566-579. |
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| 2. Kabsch,W. & Sander,C. (1983) Dictionary of protein secondary |
| structure: pattern recognition of hydrogen-bonded and |
| geometrical features. Biopolymers, 22: 2577-2637. |
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| 3. Eisenhaber, F. and Argos, P. (1993) Improved strategy in |
| analytic surface calculation for molecular systems: handling of |
| singularities and computational efficiency. J. comput. Chem. 14, |
| 1272-1280. |
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| 4. Eisenhaber, F., Lijnzaad, P., Argos, P., Sander, C., and Scharf, |
| M. (1995) The double cubic lattice method: efficient approaches |
| to numerical integration of surface area and volume and to dot |
| surface contouring of molecular assemblies. J. comput. Chem. 16, |
| 273-284. |
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| 5. Bernstein, F.C., Koetzle, T.F., Williams, G.J., Meyer, E.F., |
| Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T., and |
| Tasumi, M. (1977) The protein data bank: a computer-based |
| archival file for macromolecular structures. J. Mol. Biol. 112, |
| 535-542. |
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| 6. Kraulis, P.J. (1991) MOLSCRIPT: a program to produce both |
| detailed and schematic plots of protein structures. J. Appl. |
| Cryst. 24, 946-950. |
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| 7. Pearson, W.R. (1990) Rapid and sensitive sequence comparison |
| with FASTP and FASTA. Methods. Enzymol. 183, 63-98. |
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