1. The crystallographic problem

With the advent of Internet computing and World Wide Web technology, Web browsers have provided powerful tools for server and client-side applications. Exploiting this rapidly growing technology, the Water Analysis Package (WAP) has been developed to enable the user to calculate geometrical parameters between water oxygen atoms and a user-specified region in a given protein or nucleic acid structure. In fact, there are few stand-alone programs (for example the CONTACT module available in the CCP4 suite of programs; Collaborative Computational Project, Number 4, 1994) to calculate geometrical parameters involving water molecules and protein atoms. Furthermore, the available programs do not provide the user with flexible options to perform a specific task. These programs in general require the Protein Data Bank (PDB) (Bernstein et al., 1977) file containing the atomic coordinates, the unit-cell constants and the space-group information. To the best of our knowledge, there is no program available on the Web to perform the above task for structures deposited in the PDB or available in the public domain. At present, the PDB is maintained by the Research Collaboratory in Structural Bioinformatics (RCSB) at the Rutgers University, New Jersey, USA (Berman et al., 2000).

In view of the above, we have developed Web-based software, the Water Analysis Package (WAP), offering several useful utilities.

2. Program implementation

The program is organized into two main sections: (a) for the structures available in the PDB and (b) for three-dimensional atomic coordinates from the client machine. For the protein structures available in the PDB, the user needs to provide a four-character PDB identification code. The corresponding atomic coordinates are then retrieved from the locally maintained anonymous PDB-FTP (file transfer protocol) server, Bioinformatics Centre, Indian Institute of Science, Bangalore. The information pertaining to the calculation, such as the unit-cell constants and space group, is taken from the appropriate fields available in the PDB file. The symmetry-equivalent points for almost all the space groups are incorporated in the software itself. For non-standard space groups (for example B2), the user needs to provide the symmetry-equivalent points. The minimum and maximum distances are set to 2.5 and 3.6  Å (default values), respectively. The angle is set to 0° (by default). According to the specific requirements, the user can vary these default parameters.

For the second option (b), the user needs to upload the atomic coordinates file (PDB format) from the client machine to the server, via the Web browser. In addition, the user also needs to provide the cell constants and select the space group from a pull-down menu. The corresponding symmetry-equivalent points are retrieved from the in-built database (for standard space groups) incorporated in the software itself. After uploading the user's PDB file, the software calls the input PDB file and displays detailed information about the chains, metal ions and the inhibitor molecule in a convenient box. Users can select a chain or a set of chains or a particular region of the chain to perform the calculations.

The package provides the following options: contacts of water oxygen atoms with (i) all atoms, (ii) all protein atoms, (iii) only water oxygen atoms, (iv) all polar atoms, (v) all non-polar atoms, (vi) only nitrogen atoms, (vii) only oxygen atoms, (viii) all backbone atoms, (ix) all side-chain atoms, (x) all side-chain polar atoms, (xi) all backbone polar atoms.

The program produces a detailed output (distances and angles) with a brief summary at the end. The angle is calculated between the oxygen-donor/acceptor-bonded atoms. Information is provided about the number of water molecules and the interactions with the various regions of the protein molecule. In addition, for multi-subunit structures, the output contains information about the number of interactions with individual sub-units (Fig. 1). The program prints the `water molecule' that has no contacts (with the user-specified lower and upper cut-off distances) only for the option `All atoms in the PDB file'.

Figure 1 Sample output (water oxygen contacts for all the atoms in the PDB file) produced by the package WAP (only part of the output is shown here). The input PDB file used to create the output is 1JAC (Sankaranarayanan et al., 1996).

3. Program specification and availability

The computing engine is written using CGI/PERL (as implemented in RedHat Linux 7.2) and it can be executed on our Bioinformatics Linux server (a 1.5  GHz Pentium IV processor, 1 Gbytes of main memory). The front-end input data form is created in HTML and JavaScripts are used to facilitate user-friendly Web-browser input. The program is general and very easy to use. It runs on Windows 95/98/2000, Windows NT server, Linux and Silicon Graphics (SGI) platforms through the Netscape browser. In the trial runs, the results appear in about 15 to 20  s [for example, PDB code 1JAC (Sankaranarayanan et al., 1996) containing 592 amino acid residues with 323 water molecules]. The execution time may vary depending upon the number of atoms and the network speed. The search facility described is freely available for academic users and non-commercial organizations over the Web (at http://144.16.71.11/wap ).