GET LIG[AND] & TAR[GET] MOLECULES:
Get a thermodynamically enriched decomposition of conformational space
into metastable areas called Eigenconformations, which are weighted
by local thermodynamical properties.
Eigenconformations serve as input for comparison, docking and QSAR
of molecules using the GLAT program package.
GET GLAT, a program package for efficient thermodynamical simulation and analysis of molecules on heterogenous high performance computer platforms using Global Local Adaptive Thermodynamics . GLAT performs Hybrid Monte Carlo simulations for molecules parameterized by the MMFF force field. Uncoupling of Markov Chains on different simulation levels allows coarse to fine tuning of different parallization strategies using MPI and OpenMP. The program is running on CPU-Cluster, Intel Xeon Phi (7100 and 7200 series) and GPU .
GET CONTACT
GET PUBLICATIONS [Cordes]
Actual Activities:
Research Center for Many-core HPC at Zuse Institut Berlin
GETLIG & TAR is industry partner in the Research Center for Many-core High-Performance Computing at Zuse Institut Berlin, which aims on enhancing selected workloads with impact on the HPC community to improve performance and scalability on many-core processor technologies and platform architectures.
Former Activities:
ENHANCE
GETLIG & TAR was industry partner in the BMBF funded ENHANCE project, which aimed on a better integration and simplified usage of heterogeneous computing resources within current and upcoming computing systems.
MoSGrid
GETLIG & TAR was industry partner in the BMBF funded MoSGrid project, which focused on the configuration and provision of Grid services for molecular simulations.
Technology
GLAT samples an ensemble of metastable states in parallel. The calculation of interactions concerning the explicitly modeled water is distributed on accelerators (Xeon Phi, GPU). The result is an ensemble of conformational distributions within all metastable states discovered by GLAT.
Downloads
Get a thermodynamically enriched decomposition of conformational space
into metastable areas called Eigenconformations, which are weighted
by local thermodynamical properties.
Eigenconformations serve as input for comparison, docking and QSAR
of molecules using the GLAT program package.
GET GLAT, a program package for efficient thermodynamical simulation and analysis of molecules on heterogenous high performance computer platforms using Global Local Adaptive Thermodynamics . GLAT performs Hybrid Monte Carlo simulations for molecules parameterized by the MMFF force field. Uncoupling of Markov Chains on different simulation levels allows coarse to fine tuning of different parallization strategies using MPI and OpenMP. The program is running on CPU-Cluster, Intel Xeon Phi (7100 and 7200 series) and GPU .
GET CONTACT
GET PUBLICATIONS [Cordes]
Actual Activities:
Research Center for Many-core HPC at Zuse Institut Berlin
GETLIG & TAR is industry partner in the Research Center for Many-core High-Performance Computing at Zuse Institut Berlin, which aims on enhancing selected workloads with impact on the HPC community to improve performance and scalability on many-core processor technologies and platform architectures.
Former Activities:
ENHANCE
GETLIG & TAR was industry partner in the BMBF funded ENHANCE project, which aimed on a better integration and simplified usage of heterogeneous computing resources within current and upcoming computing systems.
MoSGrid
GETLIG & TAR was industry partner in the BMBF funded MoSGrid project, which focused on the configuration and provision of Grid services for molecular simulations.
Technology
GLAT samples an ensemble of metastable states in parallel. The calculation of interactions concerning the explicitly modeled water is distributed on accelerators (Xeon Phi, GPU). The result is an ensemble of conformational distributions within all metastable states discovered by GLAT.
Downloads
The help section is under construction.
To have real benifit of this site you have to enable webgl in your webbrowser. Try to use the latest update of your favorite browswer. The site works best with Firefox and Chrome.
If webgl is not enabled, try the following:
A short tutorial:
Use the GET button to load molecules from the PDB, PubChem or GL%T server. In case of PDB you need the entry number. For PubChem and GL&T server the syntax is a little different, namely Letter{query}, to allow differen queries to the server.
To have real benifit of this site you have to enable webgl in your webbrowser. Try to use the latest update of your favorite browswer. The site works best with Firefox and Chrome.
If webgl is not enabled, try the following:
- Internet Explorer: use the latest update.
- Firefox : try force enable WebGL.
- Chrome: try force enable WebGL.
- Safari: enable WebGL.
A short tutorial:
Use the GET button to load molecules from the PDB, PubChem or GL%T server. In case of PDB you need the entry number. For PubChem and GL&T server the syntax is a little different, namely Letter{query}, to allow differen queries to the server.
-
PubChem
- Give a C (default) for search of PubChem-id and with the brackes
-
GL&T
Impressum (Terms of Use)
Verantwortlich für den Inhalt (§ 10 Abs. 3 MDStV) ist
Dr. Frank Cordes
Bachstelzenstr. 33A, 14612 Falkensee
cordes(@)getlig.com
URL: www.getlig.com, (GETLIG&TAR (GL&T)),
This website is based on developments of 3Dmol.js and incorporates code from GLmol, Three.js, and jQuery. The code is licensed under a BSD style license. 3Dmol.js is based on WebGL and Javascript. (https://github.com/dkoes/3Dmol.js) You can embed molecular models in Web pages without using Java or plugins.
The editor is based on Javascript Code developed by Earley, C.W. and published as: CH5M3D: an HTML5 program for creating 3D molecular structures. J Cheminform 5, 46 (2013).https://doi.org/10.1186/1758-2946-5-46 The editor tool is usable under GNU General Public License version 3.0.
The authors of the getlig.com site would like to express their regard for the development of these very helpful tools.
Nutzungsbedingungen:
Alle auf dieser Website veröffentlichten Informationen wurden gewissenhaft recherchiert und sorgfältig zusammengestellt. GL&T behält sich vor, jederzeit und ohne Vorankündigung die Inhalte dieser Website zu verändern, zu erweitern oder zu entfernen. Informationen und Angebote sind daher freibleibend und unverbindlich.
Diese Website unterliegt dem Urheberrecht. Alle innerhalb der Website genannten und ggf. durch Dritte geschützten Marken- und Warenzeichen unterliegen den Bestimmungen des jeweiligen Kennzeichenrechtes und sind Eigentum der jeweiligen Besitzer.
Haftungsausschluss:
Trotz aller Sorgfalt kann GL&T für alle Verweise von dieser Website sowie Verweise auf diese keine Haftung übernehmen. GL&T ist für externe Verweise nicht verantwortlich.
Eine Haftung von GL&T für materielle oder ideelle Schäden, die durch Nutzung oder Nichtnutzung der dargebotenen Inhalte bzw. durch die Nutzung fehlerhafter oder unvollständiger Informationen verursacht werden, ist grundsätzlich ausgeschlossen.
Verantwortlich für den Inhalt (§ 10 Abs. 3 MDStV) ist
Dr. Frank Cordes
Bachstelzenstr. 33A, 14612 Falkensee
cordes(@)getlig.com
URL: www.getlig.com, (GETLIG&TAR (GL&T)),
This website is based on developments of 3Dmol.js and incorporates code from GLmol, Three.js, and jQuery. The code is licensed under a BSD style license. 3Dmol.js is based on WebGL and Javascript. (https://github.com/dkoes/3Dmol.js) You can embed molecular models in Web pages without using Java or plugins.
The editor is based on Javascript Code developed by Earley, C.W. and published as: CH5M3D: an HTML5 program for creating 3D molecular structures. J Cheminform 5, 46 (2013).https://doi.org/10.1186/1758-2946-5-46 The editor tool is usable under GNU General Public License version 3.0.
The authors of the getlig.com site would like to express their regard for the development of these very helpful tools.
Nutzungsbedingungen:
Alle auf dieser Website veröffentlichten Informationen wurden gewissenhaft recherchiert und sorgfältig zusammengestellt. GL&T behält sich vor, jederzeit und ohne Vorankündigung die Inhalte dieser Website zu verändern, zu erweitern oder zu entfernen. Informationen und Angebote sind daher freibleibend und unverbindlich.
Diese Website unterliegt dem Urheberrecht. Alle innerhalb der Website genannten und ggf. durch Dritte geschützten Marken- und Warenzeichen unterliegen den Bestimmungen des jeweiligen Kennzeichenrechtes und sind Eigentum der jeweiligen Besitzer.
Haftungsausschluss:
Trotz aller Sorgfalt kann GL&T für alle Verweise von dieser Website sowie Verweise auf diese keine Haftung übernehmen. GL&T ist für externe Verweise nicht verantwortlich.
Eine Haftung von GL&T für materielle oder ideelle Schäden, die durch Nutzung oder Nichtnutzung der dargebotenen Inhalte bzw. durch die Nutzung fehlerhafter oder unvollständiger Informationen verursacht werden, ist grundsätzlich ausgeschlossen.
3Dmol.js incorporates code from GLmol, Three.js, and jQuery and
is licensed under a BSD-3-Clause license.
* 3Dmol.js
Copyright (c) 2014, University of Pittsburgh and contributors All rights reserved.
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
* GLmol
GLmol - Molecular Viewer on WebGL/Javascript (0.47) (C) Copyright 2011-2012, biochem_fan License: dual license of MIT or LGPL3
Contributors: Robert Hanson for parseXYZ, deferred instantiation
* Three.js
Copyright (c) 2010-2012 three.js Authors. All rights reserved.
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
* jQuery
"
Copyright (c) 2011 John Resig
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
* 3Dmol.js
Copyright (c) 2014, University of Pittsburgh and contributors All rights reserved.
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
* GLmol
GLmol - Molecular Viewer on WebGL/Javascript (0.47) (C) Copyright 2011-2012, biochem_fan License: dual license of MIT or LGPL3
Contributors: Robert Hanson for parseXYZ, deferred instantiation
* Three.js
Copyright (c) 2010-2012 three.js Authors. All rights reserved.
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
* jQuery
"
Copyright (c) 2011 John Resig
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.