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...embles your current project, in terms of available information and perhaps target class, ligand chemistry, or binding site situation. Please see also the [[ * Target category: Nuclear receptor

...r proteins/genes are targetable and the subset of our small molecules that target something comes from cross-references to ZINC. You can see the ZINC cross- Unfortunately, we don’t have direct target associations between small molecules and genes in Reactome, but in some cas

* MakeDOCK automates the process of sphere and grid generation for a target. * These are required to specify the target for docking. For help preparing these files, see [[#Receptor Preparation]]

...he target is available. vHTS docks a database of small molecules against a target, often a protein, using a molecular docking program. It ranks the database vHTS has also been used for target-free ligand discovery, based on the similarity of known actives to compound

...s). Decoys refers to a set of molecules that (probably) won't bind to your target. Here are some terms: *[[Ligands]]: A set of known ligands that bind to your protein target. Often taken from papers or a database like [http://www.ebi.ac.uk/chembldb/

...easy to follow and use guide for non-specialists wishing to computational target-based ligand discovery (docking, virtual screening) techniques.

= By Target = == By Target Name ==

...are also known as scaffold hopping, and do not require a structure of the target. Instead, they use the ligand, or several ligands, and use either the shap

...hich other people have done before. For more information, please see the [[Target:CDK2]] wiki page OR please join the [http://docking.org/?q=node/12 cdk2 dis

* Search for a target based on a given UniProt accession - https://www.ebi.ac.uk/chemblws/targets * Search for a target based on a given RefSeq accession and return it in JSON format - https://ww

...nes" of the fine tranches are given priority (this is done by lowering the target partition size for the zone), such as the fertile region from H17P200 to H3 * PARTITION_NO- the line number of the target partition in the partitions.txt file

...computing how significant the sum of all pairs, between the query and the target are. The method for how the threshold is chosen depends on the fingerprint

=== Target Preparation / Calibration Problems === * Your job fails or seems to get stuck during "Target Preparation".

** Target preparation -> Prepare

* I have a protein target (structure) and I want to find ligands that bind to it. (docking) ...ve ligands that bind to a protein and I want to find more ligands for that target (multi-ABC, SEA)

Depending on the structural features of the target model, you may need to take special steps to prepare for docking. Many of t ...may well be preferable to use the non-covalently bound ligand form of the target.

Both methods are suitable for using on your own protein, providing you have a target structure (for docking) or ligand structure (for SEA). Please contact John ...e to come to the "watch me" session. Also, if you want to work on your own target, please contact John Irwin or Brian Shoichet for conversation during the me

...er enables the efficient search for the optimal DOCK parameters of a given target receptor as evaluated by the amount of enrichment witnessed in retrospectiv

...of everything an expert docker needs to know in order to perform the best target-based computational ligand discovery possible.

'''B. Comparing the interactions of different ligands with the same target'''