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• Target
  ...r which you seek new [[ligands]]. If an [[X-ray crystal structure]] of the target is available, that is often the preferred model for docking. However, struc
  483 bytes (71 words) - 03:53, 13 March 2014
• Orphan target
  An orphan target is a target for which the endogenous metabolite and physiological function is unknown.
  125 bytes (18 words) - 17:15, 11 March 2014
• Protein target
  #REDIRECT [[Target]]
  20 bytes (2 words) - 03:53, 13 March 2014
• Target:CDK2
  18 bytes (2 words) - 20:33, 8 October 2012
• Target based
  ...et-derived pharmacophore methods. There are likely to be other methods, as target crystal structures can be used in many ways.
  224 bytes (33 words) - 20:33, 8 October 2012
• Protein Target Preparation
  Protein Target Preparation
  2 KB (264 words) - 16:57, 28 August 2019
• Protein Target Preparation Updated
  16 KB (2,467 words) - 18:59, 10 October 2019
• Features of your target structure
  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.
  2 KB (310 words) - 20:24, 8 October 2012
• B. Comparing the interactions of different ligands with the same target
  3 KB (561 words) - 09:56, 13 March 2014
• DOCK Blaster:Dock PDB target
  989 bytes (164 words) - 20:02, 8 October 2012

Page text matches

• Target based
  ...et-derived pharmacophore methods. There are likely to be other methods, as target crystal structures can be used in many ways.
  224 bytes (33 words) - 20:33, 8 October 2012
• Orphan target
  An orphan target is a target for which the endogenous metabolite and physiological function is unknown.
  125 bytes (18 words) - 17:15, 11 March 2014
• Heatmap tool
  /nfs/work/teague/Projects/heatmaps/bin-target-actives.py * python bin-target-actives.py OPRD1 -o OPRD1.counts # write 2D matrix of counts to file
  613 bytes (86 words) - 20:44, 3 May 2016
• ZINC15:videos
  * [[Target target]] * [[Ligands for my target]]
  696 bytes (79 words) - 00:08, 2 October 2015
• CDK2
  This is the target page for CDK2. This is an important target.
  402 bytes (64 words) - 18:10, 8 October 2012
• Protein target
  #REDIRECT [[Target]]
  20 bytes (2 words) - 03:53, 13 March 2014
• Getting Started
  Docking requires a structure of the target to dock to. == Target structure NOT available ==
  2 KB (306 words) - 06:37, 13 March 2014
• Features of your crystal structure
  #REDIRECT [[Features of your target structure]]
  47 bytes (6 words) - 20:24, 8 October 2012
• Sphere Selector
  ...spheres with a user-defined radius of a target molecule (see sphgen). The target molecule can be anything (ie known ligand, receptor residue, etc) as long a
  514 bytes (82 words) - 04:26, 14 February 2014
• Psicquic channels
  = Target-Target Channels (tt) = = Target-Compound Channels (ct) =
  1 KB (152 words) - 23:31, 30 January 2018
• Pharmacophore-based methods
  Pharmacophore methods include both [[target based]] and [[ligand based]] methods for ligand discovery. = Target based pharmacophore methods =
  901 bytes (127 words) - 20:31, 8 October 2012
• Target
  ...r which you seek new [[ligands]]. If an [[X-ray crystal structure]] of the target is available, that is often the preferred model for docking. However, struc
  483 bytes (71 words) - 03:53, 13 March 2014
• DOCK Blaster job example
  * Target name: [[Target:target_name target_name]]
  569 bytes (67 words) - 20:02, 8 October 2012
• Quick Search Bar
  = Target = ...well as target names are supported. To force this behavior, prefix with target:
  2 KB (272 words) - 18:00, 2 May 2024
• ZINC15 todo
  * target class list and target class detail pages (TS) * target list and target detail pages (TS)
  2 KB (331 words) - 00:00, 29 July 2015
• Tool1
  * Specify first target * Specify second target
  601 bytes (92 words) - 05:05, 14 February 2014
• Beta Secretase
  Beta secretase is an important target.
  83 bytes (11 words) - 18:10, 8 October 2012
• Nailgun
  ...er/target/classes:/nfs/home/stefan/NAILGUN/nailgun-master/nailgun-examples/target/classes:/nfs/soft/jchem/jchem-19.15/lib/*" ./nailgun-client/target/ng com.facebook.nailgun.examples.HelloWorld
  2 KB (300 words) - 20:52, 18 March 2020
• ZINC Novelty Score
  ...velty of the compound with respect to known (annotated) compounds for that target. ...compound with respect to known (annotated) compounds matching a particular target pattern.
  2 KB (264 words) - 04:20, 1 October 2015
• Scaffold hopping
  ...ctives, that have a good chance of being active themselves. In contract, [[target based]] methods such as docking tend to produce a much lower rate of active ...n ligand discovery projects use some combination of [[ligand based]] and [[target based]] techniques.
  823 bytes (126 words) - 20:32, 8 October 2012
• DOCK Blaster:Tutorials
  ...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
  4 KB (523 words) - 20:02, 8 October 2012
• Reactome integration
  ...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
  1 KB (175 words) - 14:11, 6 September 2016
• Understanding MakeDOCK, which automates sphere and grid generation
  * 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]]
  3 KB (488 words) - 02:43, 13 March 2014
• Virtual screening
  ...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
  1 KB (225 words) - 20:33, 8 October 2012
• Decoy Theory
  ...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/
  3 KB (426 words) - 23:39, 3 January 2019
• Docking for non-experts
  ...easy to follow and use guide for non-specialists wishing to computational target-based ligand discovery (docking, virtual screening) techniques.
  318 bytes (38 words) - 03:43, 13 March 2014
• How to link to ZINC
  = By Target = == By Target Name ==
  4 KB (542 words) - 00:47, 10 January 2019
• Ligand based methods
  ...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
  337 bytes (53 words) - 20:29, 8 October 2012
• DOCK Blaster:4100
  ...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
  321 bytes (56 words) - 20:02, 8 October 2012
• ChEMBL API
  * 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
  1 KB (237 words) - 06:46, 13 March 2014
• Loading And Creating ZINC Partitions Automatically
  ...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
  3 KB (499 words) - 04:07, 29 May 2020
• Sea cut sum
  ...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
  383 bytes (58 words) - 15:03, 4 August 2020
• DOCK Blaster:Problems
  === Target Preparation / Calibration Problems === * Your job fails or seems to get stuck during "Target Preparation".
  2 KB (392 words) - 20:02, 8 October 2012
• DOCK Blaster:Suggestions
  ** Target preparation -> Prepare
  485 bytes (72 words) - 06:35, 14 February 2014
• Narrative
  * 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)
  1 KB (270 words) - 21:44, 9 May 2024
• Features of your target structure
  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.
  2 KB (310 words) - 20:24, 8 October 2012
• Irwin:workshop1
  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
  4 KB (578 words) - 20:27, 8 October 2012
• Dockmaster
  ...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
  462 bytes (70 words) - 22:14, 25 July 2022
• Docking for experts
  ...of everything an expert docker needs to know in order to perform the best target-based computational ligand discovery possible.
  516 bytes (63 words) - 05:12, 13 March 2014
• Building Solid Foundations for a Structure Based Design Campaign – Erice 2008
  '''B. Comparing the interactions of different ligands with the same target'''
  636 bytes (81 words) - 09:56, 13 March 2014
• DrugBank
  ...chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information.
  797 bytes (113 words) - 13:01, 21 March 2014
• DOCK Blaster:Protocols
  == Protocol D1: Dock a single ligand to a single target ==
  1 KB (209 words) - 03:51, 13 March 2014
• DOCK Blaster:Preliminaries
  ...king. You will also need to have some idea of the binding site you wish to target, as proteins often contain more than one eligible site. You may also have a ...many techniques for ligand discovery. In particular, if actives against a target are already known, the simplest way may be to simply look for analogs and d
  8 KB (1,233 words) - 20:02, 8 October 2012
• THC
  = Sources of Molecule-Target Assocations = ...has molecule-target and molecule-indication mappings, and thus implicitly target-indication mappings.
  4 KB (581 words) - 20:33, 8 October 2012
• New zinc15 questions
  7. What are the tool compounds for each target?
  550 bytes (89 words) - 20:32, 12 July 2015
• Asthma
  = No target structure available =
  2 KB (205 words) - 18:10, 8 October 2012
• Allowing NFS through iptables/firewalld
  target: default target: default
  2 KB (220 words) - 16:27, 2 July 2018
• DOCK Blaster:Prepare Input
  ...ptionally have additional information about actives and inactives for this target. This page provides a quick overview of preparing input files for docking. *1. Specify a target in PDB or mol2 format.
  6 KB (944 words) - 20:02, 8 October 2012
• DOCK Blaster:Progress Bar
  ...ix stages, some with several substages, as follows: Preparer, Scrutinizer, Target Preparation, Calibration, Docking, and Results. = Target Preparation =
  4 KB (686 words) - 20:02, 8 October 2012
• Building Solid Foundations for a Structure Based Design Campaign – Workshop handout Erice 2008
  '''[[B. Comparing the interactions of different ligands with the same target]]'''
  665 bytes (85 words) - 09:56, 13 March 2014