StoneHinge - Predicts protein hinges for a given PDB file
stonehinge [OPTIONS] PDBFILE
Options:
-w Keep water molecules present in the PDB
-t Do not truncate modified residues and keep all heteroatoms
-c Ignore chain ID's (force prediction on
multi-chain proteins)
-d[=NAME] Place the output files in the specified directory
-p[=NAME] Place the output files in the current directory prefixed
with the protein name
-k Keep the temporary directory created during processing
-a[=NAME] Keep all files created during processing and place them
in the specified directory
-l=DIR Place any error logs in the specified directory
-e=NAME Include the given protein name in all error log file names
--nol Do not keep error logs
-h Print help and exit
StoneHinge is a hinge prediction algorithm that peforms a network-based analysis of a single protein structure to detect hinge regions. StoneHinge incorporates both ProFlex, which uses the FIRST constraint counting algorithm, and DomDecomp, which uses Gaussian Normal Mode analysis.
For the StoneHingeP (ProFlex) predictions, StoneHinge finds the two largest rigid domains in the protein at each bond coordination level. The "native" state is taken to be the coordination level with the biggest second-largest rigid domain. The hinges are then taken to be any residues between these two domains.
For the StoneHingeD (DomDecomp) predictions, StoneHinge identifies hinges as residues in between domains or at domain boundaries. The StoneHingeP and StoneHingeD predictions are then combined by taking any StoneHingeD hinge within five residues of a StoneHingeP hinge.
When analyzing the file protein.pdb, all output files will be placed in a subdirectory named protein_sh. (See -p and -d for ways to change this behavior.) These files are generated by Proflex and more information about them can be found in the Proflex manual. The output consists of:
clust.htm A Chime webpage containing Proflex's rigid cluster
analysis
clust.pdb The PDB file used by clust.htm
decomp A Proflex data file containing cluster
decompositions
dil.pdf A hydrogen-bond dilution plot generated by Proflex
proflexdataset A Proflex datafile containing all atoms and bonds
flexb.pdb A PDB file contianing the flexibility index of each
atom in the b-factor column
domdecomp.out The output of the DomDecomp prediction. Note that
residues in this file are numbered consecutively
beginning with 1, regardless of the numbering
in the PDB file.
If Gromacs, Proflex, or DomDecomp cannot successfully process the protein, an error message will be displayed giving the name of the program that failed. An error log will be then be created in the current directory containing the standard output and standard error of the program. (See -l, -e, and --nol for ways to change this behavior.)
IMPORTANT: Currently, StoneHinge only works on single chain proteins. If a multi-chain protein is given as input, StoneHinge cannot differentiate between residues of the same number on different chains and will not take chain boundaries into account when predicting hinges.
stonehinge 1DVR.pdb
Predict hinges of file 1DVR.pdb. Output will be placed in the 1DVR_sh directory.
stonehinge -p akinase 1DVR.pdb
Predict hinges of file 1DVR.pdb. Output will be placed in the current directory and named akinase.dil.pdb, akinase.clust.htm, etc.
stonehinge -d akinase 1DVR.pdb
Predict hinges of file 1DVR.pdb. Output will be placed in the akinase directory.
Keep all water molecules in the input. The default it to ignore all water molecules. Ideally, predictions should be run using only internal water molecules; all external water molecules should be removed as these increase running time and tend to over-rigidify the surface of the protein. Internal water molecules can be found using a program such as Pro_Act. However, there are generally few differences in the predicted residues when all water molecules are ignored.
By default, StoneHinge will remove all heteroatoms and truncate all modified residues to alanine or glycine, which does a ``quick-and-dirty'' cleanup of the protein. Heteroatoms such as ligands generally over-rigidify the protein as they tend to lock it into the closed state. Gromacs, which is used to add hydrogens, cannot handle ions or modified residues without additions to the Gromacs topology database. For more accurate predictions, the -t option can be used after manually removing the ligands and changing modified residues back to their corresponding standard residue.
Ignore chain ID column in the PDB file. Currently, StoneHinge only works on single-chain proteins. This option will force StoneHinge to process a multi-chain protein by ignoring the chain ID column. Note that StoneHinge will not be able to differentiate between two residues on different chains with the same residue number. Use of this option is not recommended.
Place all output files in the specified directory. For example, -d=hivprot will create an hivprot directory containing files such as proflexdataset and dil.pdf. If no name is give, the filename of the input PDB file followed by _sh will be used. (This is the default behavior of the program.) This option cannot be used at the same time as -p or -a.
Place all output files in the current directory and prefix them with the given name. For example -p hivprot will create the output such as hivprot.proflexdataset and hivprot.dil.pdf. If no name is given, the filename of the input PDB file will be used. This option cannot be used at the same time as -d or -a.
Keep all files created during the StoneHinge analysis, but move the output files to the location specified by -p or -d (or the default location). The non-output files will be placed in a directory of the input PDB filename followed by _sh_temp. This option cannot be used at the same time as -a.
Keep all files created during the StoneHinge analysis and place them in the specified directory. No files will be moved to an output directory. If no name is given, the filename of the input PDB file followed by _sh will be used. This option cannot be used at the same time as -p, -d, -k, or --nol.
By default, if an error occurs with Gromacs or Proflex, an error log will be created (consisting of standard out and standard error from the failed program) and placed in the current directory. This option allows you to specify a different directory in which to place the error log. The filename of the log consists of the protein name (specified with the -n option) followed by the name of the program that failed, with a .log extension.
Allows you to specify the name of the protein for used in naming the error log file (see the -l option). If this option is not used, the protein name will be the prefix or directory name (as given with -p or -d). It neither a prefix nor a directory is given, the file name will be used.
Do not keep an error log if a Gromacs or Proflex fails. The error logs will still be created in the temp directory. This option cannot be used at the same time as -a.
Print this help and exit.
StoneHinge will not work properly if run from a directory with a single quote (') in the path.
StoneHinge programmed by Kevin Keating, Yale University, 2008. Kevin.Keating@yale.edu
StoneHinge developed by Kevin Keating, Samuel Flores, Mark Gerstein, and Leslie Kuhn.
ProFlex developed by Donald Jacobs, A.J. Rader, Leslie Kuhn, and M.F. Thorpe.
DomDecomp developed by Sibsankar Kundu, Dan Sorensen, and George Phillips, Jr.
Reference: Keating KS, Flores SC, Gerstein MB, Kuhn LA (2009). StoneHinge: Hinge Prediction by Network Analysis of Individual Protein Structures. Protein Science 18: 359-371.