PROMOLP FEATURES, HOW TO INSTALL IT, AND A BRIEF INTRODUCTION TO OPERATIONS

PROMOLP (PROtein MOLecular Parameters) computes the following parameters from a protein primary structure information: molecular weight, partial specific volume, theoretical hydration, hydrated and unhydrated molecular volumes and radii of the equivalent spheres, theoretical extinction coefficient at 280 nm, theoretical differential increment of the refractive index (dn/dc), average hydrophobicity and related functions, isoelectric point and net charge as a function of pH. The sequence can be enter manually or automatically translated from the SWISS-PROT data bank format. It could be displayed and printed in the one-letter code with superimposed the additional informations entered by the user, such as position of free-SH groups, of phospho-serines, -threonines, and -tyrosines, and of carbohydrate moieties, of proteolytic cleavage points and intron/exon boundaries. The whole sequence or parts of it, selected with the help of the additional informations displayed, can then be analyzed.

You will download a zip file containing a directory with the installation files (run setup.exe), and some updated reference files. After installation, just substitute the def* files installed by the program with the other ones present in the zip file. 
Available for download are also a PROMOLP-formatted and a SWISS-PROT-formatted files as examples. In case you need to cite PROMOLP, here's the reference

Spotorno, B., Piccinini, L., Tassara, G., Ruggiero, C., Nardini, M., Molina, F.,
and Rocco, M. (1997). BEAMS (BEAds Modelling System) a set of computer
programs for the generation, the visualization and the computation of the
hydrodynamic and conformational properties of bead models of proteins.
Eur. Biophys. J. 25, 373–384; Erratum (1997) 26, 417.

As for running PROMOLP, unfortunately there's no help provided, but the operations are very simple and should be quite evident. 
Basically, you need to enter a sequence, either manually by clicking on buttons with the amino acids names, or by importing a properly formatted sequence file (very easy to prepare using just a text editor, see the example file). Once you have the sequence in, you are asked to add the various prosthetic groups available, like number and position of phosphoserines, phosphothreonines and phosphotyrosines, and carbohydrates chains. For the latter, of course you need to know the composition (available residues: MAN. GLC, GAL, GLCNAC, GALNAC, FUC, NEUNAC). You are also asked to enter number and position of free SH. In this respect, PROMOLP works the other way in respect to SEDENTERP, it assumes that all cysteines are in disulfide bonds unless you specify which ones are free. If you don't know the position of them, and of all the other modifications, it will matter only if you analyze a part of the sequence, in which case it won't be able to carry on the correct info.
You could also enter some annotations, like exon boundaries and proteases cut points, that will be visualized with the sequence. Computations of the parameters can be done on the entire file, or on a part of it. An editor ("Modify" menu) allows modifications to be made to an already entered sequence (adding, deleting, changing aa residues).

PROMOLP was developed using Visual Basic for Windows. To store and retrieve the data, it utilizes a file format in which the amino acid (aa) sequence is placed in strings of up to 79 characters containing up to 40 aa each, in the one-letter code and separated by a space. In the first line of a PROMOLP file (automatically recognized if the filename contains the extension *.pro) is placed a string used for identification ("Title"), followed by a second line containing the total number of aa, the number of aa strings, and the position of the first string in the original sequence (used to mantain the original numbering if parts of a sequence are analyzed and stored as such). The strings containing the aa sequence follows, at the end of which are stored all the other informations: in a line are seven numbers corresponding respectively to the number of free -SH groups, of phospho-serines, of phospho-tyrosines, of phospho-threonines, of carbohydrate chains, of proteases for which proteolytic cleavage points have been entered, and of intron/exon boundaries. If any of the first four number is different from 0, the position(s) in the sequence for the free -SH, etc., is then recorded on separate lines. Next, the position in the sequence and the number of each sugar unit are recorded on separate lines for the carbohydrate chains, if present, followed by a line containing name, symbol and number of cleavage points for each entered protease, with the relative cleavage positions marked in the following line. Finally, the position of each exon's end is recorded sequentially. The last number in the file indicates if the amino-terminal is blocked or not (0/1). This file structure was derived from earlier versions of the program, but was retained for compatibility and because permits an easy editing of the data with a normal word processor, if the editing capabilities of PROMOLP are not found to be adeguate.
The physico-chemical data for the aa and the prosthetic groups are stored in six “default” (DEF*) separate files, containing respectively the molecular weights (DEFMW), the molar volumes (DEFMV), the theoretical number of water molecules bound for each group (DEFHYD), the deltaG of side-chain transfer from CH3CH2OH to H2O (DEFDELTA, only for the aa moieties), the molar refraction of the residues and the refractive index of the solvent to which the dn/dc computation is referred to, and, only for the ionizable residues, their pKas (DEFPK). The files are editable directly from PROMOLP through a “Edit parameters” feature.