AQUA

Description

AQUA is capable of calculating the level of completeness of NOEs of an experimental set of NOEs on the basis of a three-dimensional structure of the molecule. The easiest way to try the completeness module of AQUA is via one of the AQUA servers mentioned below. The service can handle NOE restraints from most NMR software packages (e.g. X-PLOR, MSI, DYANA and AQUA).

AQUA currently is not able to handle ambiguous NOEs of the type commonly used by programs such as AMBER, ARIA, CNS, and SANE. Please inform me if you have a parser for this type of NOEs that can handle the full set of formats used for ambiguous NOEs.

Output from AQUA can be read and visualized by PROCHECK-NMR, a program in the PROCHECK suite for assessing the stereochemical quality of protein structures. The PROCHECK suite was developed in the Biomolecular Structure and Modelling Group (prof. Thornton), University College, London (Procheck WWW info).

AQUA was developed as part of the Biotech Validation Project. This project was a collaborative effort of 6 European laboratories, aimed to produce a coordinated and linked set of software modules that integrate a number of existing as well as new procedures and protocols for recording, communicating and validating the models resulting from 3-D structural studies on biomolecules. The modules should also provide assessment of the intrinsic quality of the experimental data and the agreement between such data and the derived atomic models. An important part of the effort was directed at developing validation criteria by a systematic analysis of published structures. Software was made available to the community, by distributing source code and data files.

The Validation Project was funded by the BIOTECH program of DGXII of the Commission of the European Union, under contract numbers BIO2CT-920524 and BIO4-CT96-0189.

Documentation

• Procheck-NMR/AQUA on-line manual (somewhat dated)
• Please read the following documents to get an idea of whether aqua will be able to serve your needs before you actually do the install.
• README
• HOW_TO_INSTALL
• HOW_TO_USE
• NEW
• The AQUA web server (described below) has its own documentation.

Web server

Source code

An ANSI C  compiler is needed for successful compilation (ANSI style function declarations). The nawk implementation should understand the -v option and calls to toupper; on some systems you may have to install gawk, the GNU version of nawk (see documentation from command: qhelp gawk).

Although the code should run on non-Unix systems too, all scripts provided with the distribution are Unix-only (csh, nawk/gawk). Users of e.g. VAX/VMS will have to set up their own processing scripts. Conversion of restraint files is done completely via scripts.

If you encounter any problems, but also if you successfully installed the program, I would like to hear from you. If relevant, please mention the type of computer and operating system you are using. New AQUA releases will be mentioned on the BMRB mailing list. I welcome suggestions about possible additions and improvements to AQUA so please feel free to mail me.

The latest version of AQUA (3.2) is available here. Some older versions of AQUA are available still available but only on request. Users are no longer requested to register. NOTE: If you want to use Aqua in conjunction with Procheck-NMR you have to obtain it (version 3.4 or higher) separately.

External contributions

• Two scripts for splitting (splitpdb) and joining (joinpdb) MODELs in a PDB file.
• The patchXPLORpdb script for modifying an XPLOR PDB-file to comply better with the PDB format definition.

The AQUA modules qconvert and aq2x can be used to convert distance restraint files from/to several formats, including XPLOR, BIOSYM and DIANA. Currently, support for torsion angle restraints is limited. The qconvert module converts torsion angle restraints TO internal AQUA format. These can be converted to XPLOR using the new aq2xplor-tors script.

Referring to AQUA

• Laskowski R.A., Rullmann J.A.C., MacArthur M.W., Kaptein R. & Thornton J.M. (1996). "AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR". J. Biomol. NMR 8, 477-486.
• Doreleijers J.F., Rullmann J.A.C. & Kaptein R. (1998). "Quality assessment of NMR structures: a statistical survey". J. Mol. Biol. (1998) 281:149-164.
• Doreleijers J.F., Raves M.L., Rullmann J.A.C. & Kaptein R. (1999). "Completeness of NOEs in proteins, a statistical analysis of NMR data". J. Biomol. NMR (1999) 14, 123-132.

Sponsors

Contact the author for help, when required.