RAISE
cRAISE
Overview
cRAISE is a classical structure-based screening tool based on the RAISE (=RApid Index-based Screening Engine) technology. The triangle-descriptor abstraction of the target and small molecules allows for fast non-sequential screening of millions of compounds. It supports knowledge-based virtual screening by utilizing pharmacophore constraints and library profiles. Moreover, it considers reasonable protonation and tautomeric states of the target and ligands during the virtual screening process.
Download
cRAISE will be available soon for Linux-based operating systems (free for academic users). The ZBH provides a dynamically linked Linux version.
Limitations
cRAISE is still in development status.
People and references
cRAISE has been developed by Angela M. Henzler in the research group of Prof. Matthias Rarey at the Center for Bioinformatics of the University of Hamburg based on work of Jochen Schlosser (Schlosser, J., Rarey, M. (2009). Beyond the Virtual Screening Paradigm: Structure-Based Searching for New Lead Compounds. Journal of Chemical Information and Modeling, 49(4):800-809.) Sascha Urbaczek, Matthias Hilbig, and Stefan Bietz substantially contributed to this work.
iRAISE
Overview
iRAISE is an inverse screening tool based on the RAISE (=RApid Index-based Screening Engine) technology. The triangle-descriptor abstraction of proteins and molecules allows fast non-sequential screening of thousands of target structures. Scoring measures applied for selectivity considering the reference ligand and coverages of the pocket and the ligand pose support inter-protein ranking.
Download
iRAISE is freely available for academic users for Linux, Windows and Mac OS X. Non-academic users can get an evaluation licence free of charge. All feedback (iraise(at)zbh.uni-hamburg.de) is highly appreciated.
iRAISE is part of the AMD tools software bundle. To download iRAISE, register at https://software.zbh.uni-hamburg.de.
Limitations
iRAISE is still in development status.
PEOPLE AND REFERENCES
iRAISE has been developed by Karen Schomburg, the RAISE technology is a joint development of Sascha Urbaczek, Angela Henzler and Karen Schomburg in the research group of Prof. Matthias Rarey at the Center for Bioinformatics of the University of Hamburg based on work of Jochen Schlosser (Schlosser, J., Rarey, M. (2009). Beyond the Virtual Screening Paradigm: Structure-Based Searching for New Lead Compounds. Journal of Chemical Information and Modeling, 49(4):800-809.)
Please cite iRAISE with: Schomburg, K. T.,Bietz, S., Briem, H., Henzler, A.M., Urbaczek, S., Rarey, M. Facing the Challenges of Structure-based Target Prediction by Inverse Virtual Screening, J. Chem. Inf. Model. (2014) http://dx.doi.org/10.1021/ci500130e
mRAISE
Overview
mRAISE is a tool for ligand-based virtual screening based on the RAISE (=RApid Index-based Screening Engine) technology. The triangle-descriptor abstraction of small molecules allows fast non-sequential screening of millions of compounds. Calculated alignments are scored using a Gaussian-type scoring function which scores the general shape overlap as well as the compatibility of physicochemical features of aligned molecules.
Download
mRAISE is currently available for Linux-based operating systems (free for academic use). mRAISE is part of the AMD tools software bundle. To download mRAISE, register at https://software.zbh.uni-hamburg.de
Limitations
mRAISE is still in development status.
PEOPLE AND REFERENCES
mRAISE has been developed by Mathias M. von Behren, the RAISE technology is a joint development in the research group of Prof. Matthias Rarey at the Center for Bioinformatics of the University of Hamburg based on the work of Jochen Schlosser (Schlosser, J., Rarey, M. (2009). Beyond the Virtual Screening Paradigm: Structure-Based Searching for New Lead Compounds. Journal of Chemical Information and Modeling, 49(4):800-809.)
Please cite mRAISE with: von Behren, M.M., Bietz, S., Nittinger, E., and Rarey, M. (2016).mRAISE: an alternative algorithmic approach to ligand-based virtual screening, Journal of Computer-Aided Molecular Design, in press