Flare™ Docking is a node to run docking and scoring experiments using the Lead Finder™ docking algorithm, now fully integrated in Flare.
The Lead Finder docking engine combines a genetic algorithm search with local optimization procedures, which make it efficient in coarse sampling of ligand poses and, following refinement, in providing promising docking solutions. Lead Finder generates docked ligand poses starting from the 3D structure of an accurately prepared protein structure (either experimentally derived by X-ray or modeled by homology) and one or more 3D ligand structures. You can use Flare to prepare your protein. Lead Finder assumes that the protein is rigid and analyses the possible conformations of the ligand by rotating functional groups along each freely rotatable bond.
Three different scoring functions are employed and optimized for the accurate prediction of 3D docked ligand poses (LF Rank Score), protein-ligand binding energy (LF dG) and rank-ordering of active and inactive compounds in virtual screening experiments (LF VSscore).
The Flare Docking node supports covalent docking for predicting the binding pose and interactions of covalent inhibitors, a class of ligands which derive their activity by forming a covalent bond with the target while making at the same time a network of non-covalent interactions with the active site. The Lead Finder docking algorithm is used in a workflow similar to that of standard docking, but which enables to specify a residue which will covalently bind the docked ligands. The ligands to be docked must be drawn to include an appropriate bond-forming functional group, also called a covalent warhead. These are electrophilic groups of low chemical reactivity that, after non-covalently binding to the target protein, are positioned near a specific nucleophilic residue in the active site to which they react rapidly to form a bond. Please refer to the Flare manual or contact us at support@cresset-group.com for a list of the currently supported covalent warheads.
For those docking experiments where the pose of a ‘template’ ligand is known, this information can be used to bias the docking results for congeneric compounds. When using template docking, the molecules to be docked are aligned by substructure to the template ligand, and the aligned conformation is used to seed the docking run, generally leading to improved docking results. Note that this option is not available for covalent docking.
This node wraps the Flare executable 'pyflare', which must be installed with a valid license for this node to work. If this is installed in the default location on Windows, then it should be found automatically. Otherwise, you must either set the 'Cresset Home' preference setting or the CRESSET_HOME environment variable to the base Cresset software install directory. You may also set the 'pyflare Path' preference setting or the CRESSET_PYFLARE_EXE environment variable to point directly at the executable itself.
The ‘Flare Docking’ node can be configured to use additional resources to perform calculations. The time taken for the node to run will be drastically reduced using the Cresset Engine Broker™. To use this facility either set the 'Cresset Engine Broker' preference setting or set the CRESSET_BROKER environment variable to point to the location of your local Engine Broker. If you do not currently have the Cresset Engine Broker then contact Cresset (enquiries@cresset-group.com) for pricing on local and cloud based brokers.
For more information visit www.cresset-group.com or contact us at support@cresset-group.com.
"A LEU 10" H h w "A LYS 12" NZ c s
You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.
To use this node in KNIME, install the extension Cresset KNIME Nodes from the below update site following our NodePit Product and Node Installation Guide:
A zipped version of the software site can be downloaded here.
Deploy, schedule, execute, and monitor your KNIME workflows locally, in the cloud or on-premises – with our brand new NodePit Runner.
Try NodePit Runner!Do you have feedback, questions, comments about NodePit, want to support this platform, or want your own nodes or workflows listed here as well? Do you think, the search results could be improved or something is missing? Then please get in touch! Alternatively, you can send us an email to mail@nodepit.com, follow @NodePit on Twitter or botsin.space/@nodepit on Mastodon.
Please note that this is only about NodePit. We do not provide general support for KNIME — please use the KNIME forums instead.