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AQUA


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OS: Linux

License: Freeware





AQUA is a suite of programs for Analyzing the QUAlity of biomolecular structures that were determined via NMR spectroscopy. AQUA was initially developed by Ton Rullmann and Jurgen Doreleijers in the NMR Spectroscopy Department, Bijvoet Center for Biomolecular Research, Utrecht, The Netherlands. It is currently maintained and expanded by Jurgen Doreleijers at the BioMagResBank, University of Wisconsin-Madison, USA. AQUA (starting with version 3.0) 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.

http://nmr.cmbi.ru.nl/~jd/aqua/



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