www.bioinf.org.uk : Dr. Andrew C.R. Martin's Group at UCL

ProFit (pronounced Pro-Fit, not profit!) is designed to be the ultimate program for performing least squares fits of two or more protein structures. It performs a very simple and basic function, but allows as much flexibility as possible in performing this procedure.

The program will output an RMS deviation for the fitted regions and the fitted coordinates. RMS deviations over alternate zones and atoms may also be calculated. Thus the zones for calculating the RMS deviation can be different from those used for fitting.

This server provides ProFit's most basic function, the superimposition of two protein structures with provision for entering the zones over which the fitting and RMS calculation is performed. Profit fits the mobile structure coordinates to the reference structure.

The two files submitted in this section are the reference and mobile structures which should be in Protein Databank (PDB) format.

By default, ProFit does not read HETATM records from PDB files. This may be changed by ticking the Include Hetatms checkbox in the Fit Details section. While optimised for proteins, non-protein structures may also be fitted if they are stored in the standard PDB format. Atoms with coordinates of 9999.00, 9999.00, 9999.00 will be ignored during all calculations allowing atoms with undefined coordinates to be handled.

The fit regions for ProFit are specified in this section.

By default, ProFit fits all atoms in the mobile structure to the reference structure. Fitting over user-specified zones however can be performed by specifying the fit zones in this section.

Please note that the fit zones for both the reference and mobile structures must have the same number of atoms. It is possible to fit non-identical sequences gong to the Fit Details section and setting ProFit to fit only on backbone atoms or alpha carbons.

To add a fitting zone click on "Add Zone".

The regions to be fitted are specified by chain identifier, the start residue and the stop residues. The first three inputs are the chain identifier, start residue and stop residue for the reference structure. The second three inputs are the chain identifier, start residue and stop residue for the mobile structure. If the mobile structure region is not specified then it is assumed to have the same numbering as the reference structure.

If the chain identifier is omitted then the the zone is applied to the first chain of the file. If only the chain identifier is entered then the whole chain will be selected. By default, ProFit is not case sensitive so entering either "A" or "a" as the chain identifier will specify chain "A". ProFit can me made case sensitive using the "Case Sensitive" check box in the "Fit Details" section.

To remove a region, click on "Remove".

The user-specified RMS regions for ProFit are entered in this section.

By default, ProFit calculates the RMS deviation for the fitted regions of the reference and mobile structures. The RMS deviation over user-specified zones however can be found by specifying the zones in this section.

Please note that the RMS-calculation zones for both the reference and mobile structures must have the same number of atoms. It is possible to find the RMSd for non-identical sequences by going to the Fit Details section and setting ProFit to calculate the RMSd only on the backbone atoms or alpha carbons.

To add a zone click on "Add Zone".

To remove a zone, click on "Remove".

	Fit Options:	Iterative Fitting Include Hetatms Case Sensitive
	Fit Atoms:	All Atoms Alpha Carbons Backbone
	RMSD Atoms:	All Atoms Alpha Carbons Backbone Same as Fit atoms
	Centre of fitting:	:
	Output coordinates:	Centre of Fit Origin

Fit Options

Iterative fitting updates fit zones to obtain the best fit between two proteins. After the initial fit on the specified zones, the fitting zones are updated such that residue pairs with C-alpha atoms within three Angstroms are included and those more distant are excluded. The optimum set of equivalences is obtained using a dynamic programming method.

Note this method fits on alpha carbons only and the Fit Atoms options below will have no affect on the fitting.

Include Hetatms. By default, ProFit does not read HETATM records from the input files. This may be changed by selecting this option.

Case sensitive allows for lowercase chain identifiers. By default, ProFit is (mostly) case insensitive allowing the user to enter either "a" or "A" to indicate chain "A".

Fit Atoms and RMSD Atoms

The Fit Atoms options allow the user to select a subset of atom types to fit on. By default, ProFit fits on all atom types.

RMSD atoms sets the atoms types used to calculate the user-defined RMSd. By default the user RMSd is calculated on the same atom types used in fitting.

Center of fitting

The center of fitting option centres the fit around a residue in the reference protein structure and the corresponding residue in the mobile structure rather than the centres of geometry of the (fitting zones of the) proteins.

The centre residue of the reference structure is specified by entering the chain ID and residue number of the the matching residue in the mobile structure is specified in the same manner. If the mobile residue is omitted then the numbering is same for both structures.