Desert Scientific Software Products




Proasis2 - Protein Structure Database and Visualisation SystemProasis2 logo

Proasis2 is a protein structure database and visualisation system for drug discovery developed in collaboration with several major pharmaceutical companies.

How Proasis2 Works

Key Features

Proasis2 makes the most valuable and frequently used molecular modelling tasks as routine as searching the internet, for example. It empowers chemists to explore their own ideas and it can free up modellers' time so that they can concentrate on the more sophisticated problems in drug discovery.

Proasis2 Product Brochure (.doc).

For more information, please view slides here from a recent presentation on Proasis2.

The latest update of Proasis2, version 2009, was released Sep. 2009. A 90-day trial version is available upon request.

For research organisations based in Japan, please contact Mr.Syuinichi Ozawa, Infocom Corporation, Bioscience Department, Life Science Division, Mitsui-Kaijou Annex, 3-11 Kanda-Surugadai, Chiyoda-ku, Tokyo, 101-0062, Japan, e-mail: s.ozawa@infocom.co.jp




ViewContacts - Identify Protein-Ligand Interactions

ViewContacts is software for helping chemists, modelers, and crystallographers gain a better understanding of the non-covalent interactions in protein-ligand complexes.

ViewContacts identifies all commonly occurring interactions types, including hydrogen bonding, ionic pairs, and van der Waals contacts, and many, less well understood types, including:

An important component of ViewContacts is the handling of solvation. It enables the easy identification of unfavorable interactions due to desolvation, the separation of buried and solvated contacts, the viewing of water-mediated protein-ligand hydrogen bonds, and the ranking of binding site water molecules.

ViewContacts was developed in collaboration with one of the world's leading pharmaceutical research companies, F. Hoffmann La-Roche, Basel, Switzerland, over several years. The software includes the following features:

The application is a stand-alone command line tool that runs under Linux. For more information, please see slides from a recent presentation on ViewContacts

A free evaluation is available upon request.




Spinifex - Chemical Similarity SearchingSpinifex logo

Spinifex is advanced chemical similarity software that uses a graph-based approach. Spinifex rapidly computes the Maximum Overlapping Set (MOS) of a pair of chemical structures. The MOS is a generalisation of the Maximum Common Subgraph (MCS) and can be thought of as the largest set of substructures that two compounds share. Molecular comparisons based on the MOS are very useful for clustering chemically related compounds [1].

Spinifex has been fine-tuned specifically for handling molecules relevant to medicinal chemistry. The methods used for handling rings, for differentiating atom types, for measuring similarity, and for generating meaningful clusters, have been optimised to meet the needs of HTS data analysis, lead discovery and lead optimisation.

The application is a command line tool that runs under Linux. It can be executed on a single processor computer or in parallel, distributed over multiple computers using PVM. Also available is a Web based tool for HTS Data analysis which automatically runs Spinifex and clustering software from a web page and loads output into a spreadsheet.

In additional to chemical graph matching, Spinifex includes software for: creating molecular alignments, hierarchical clustering, viewing multiple molecules in PyMol and RasMol, and utilities for managing and manipulating sdf files.

For more information, please view slides here from a recent presentation on Spinifex.

The latest update of Spinifex, version 2.9, was released May 2008. A free evaluation version is available upon request.

[1] 'A Robust Clustering Method for Chemical Structures', M. Stahl, H. Mauser, M. Tsui, N.R. Taylor, J. Med. Chem, 2005, 48 (13), 4358-4366.




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