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- ...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, struc483 bytes (71 words) - 03:53, 13 March 2014
- ...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
- 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
- #REDIRECT [[Target]]20 bytes (2 words) - 03:53, 13 March 2014
- 18 bytes (2 words) - 20:33, 8 October 2012
- Protein Target Preparation2 KB (264 words) - 16:57, 28 August 2019
- 16 KB (2,467 words) - 18:59, 10 October 2019
- 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
- 3 KB (561 words) - 09:56, 13 March 2014
- 989 bytes (164 words) - 20:02, 8 October 2012
Page text matches
- ...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
- 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
- /nfs/work/teague/Projects/heatmaps/bin-target-actives.py * python bin-target-actives.py OPRD1 -o OPRD1.counts # write 2D matrix of counts to file613 bytes (86 words) - 20:44, 3 May 2016
- * [[Target target]] * [[Ligands for my target]]696 bytes (79 words) - 00:08, 2 October 2015
- This is the target page for CDK2. This is an important target.402 bytes (64 words) - 18:10, 8 October 2012
- #REDIRECT [[Target]]20 bytes (2 words) - 03:53, 13 March 2014
- Docking requires a structure of the target to dock to. == Target structure NOT available ==2 KB (306 words) - 06:37, 13 March 2014
- #REDIRECT [[Features of your target structure]]47 bytes (6 words) - 20:24, 8 October 2012
- ...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 a514 bytes (82 words) - 04:26, 14 February 2014
- = Target-Target Channels (tt) = = Target-Compound Channels (ct) =1 KB (152 words) - 23:31, 30 January 2018
- 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
- ...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, struc483 bytes (71 words) - 03:53, 13 March 2014
- * Target name: [[Target:target_name target_name]]569 bytes (67 words) - 20:02, 8 October 2012
- = Target = ...well as target names are supported. To force this behavior, prefix with target:2 KB (272 words) - 18:00, 2 May 2024
- * 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
- * Specify first target * Specify second target601 bytes (92 words) - 05:05, 14 February 2014
- Beta secretase is an important target.83 bytes (11 words) - 18:10, 8 October 2012
- ...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.HelloWorld2 KB (300 words) - 20:52, 18 March 2020
- ...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
- ...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
- ...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 receptor4 KB (523 words) - 20:02, 8 October 2012
- ...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 cas1 KB (175 words) - 14:11, 6 September 2016
- * 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
- ...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 compound1 KB (225 words) - 20:33, 8 October 2012
- ...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
- ...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
- = By Target = == By Target Name ==4 KB (542 words) - 00:47, 10 January 2019
- ...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 shap337 bytes (53 words) - 20:29, 8 October 2012
- ...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 dis321 bytes (56 words) - 20:02, 8 October 2012
- * 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://ww1 KB (237 words) - 06:46, 13 March 2014
- ...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 file3 KB (499 words) - 04:07, 29 May 2020
- ...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 fingerprint383 bytes (58 words) - 15:03, 4 August 2020
- === Target Preparation / Calibration Problems === * Your job fails or seems to get stuck during "Target Preparation".2 KB (392 words) - 20:02, 8 October 2012
- ** Target preparation -> Prepare485 bytes (72 words) - 06:35, 14 February 2014
- * 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
- 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
- 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 me4 KB (578 words) - 20:27, 8 October 2012
- ...er enables the efficient search for the optimal DOCK parameters of a given target receptor as evaluated by the amount of enrichment witnessed in retrospectiv462 bytes (70 words) - 22:14, 25 July 2022
- ...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
- '''B. Comparing the interactions of different ligands with the same target'''636 bytes (81 words) - 09:56, 13 March 2014
- ...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
- == Protocol D1: Dock a single ligand to a single target ==1 KB (209 words) - 03:51, 13 March 2014
- ...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 d8 KB (1,233 words) - 20:02, 8 October 2012
- = 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
- 7. What are the tool compounds for each target?550 bytes (89 words) - 20:32, 12 July 2015
- = No target structure available =2 KB (205 words) - 18:10, 8 October 2012
- target: default target: default2 KB (220 words) - 16:27, 2 July 2018
- ...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
- ...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
- '''[[B. Comparing the interactions of different ligands with the same target]]'''665 bytes (85 words) - 09:56, 13 March 2014
- ...low each compound we show affinity for this target, affinity for next best target (which can be higher), and purchasability (50=premier vendor, 40=in stock v3 KB (461 words) - 19:46, 3 November 2016
- ...en using an onblur() function to AJAX load a js based captcha into the div target, which then set a variable which indicated authentication before the form p3 KB (496 words) - 22:39, 4 January 2019
- ...control of the hypothalamus-pituitary-adrena (HPA) axis, and thus MR is a target for drug discovery. ...ght mouse clicking and selecting "save link as". If you are using your own target, you must prepare the files yourself (see [[DOCK Blaster:Input Preparation6 KB (878 words) - 03:24, 12 March 2014
- ...ate for general readership, it should have one or more [[:Category:Roles | target consituencies]] assigned.1 KB (200 words) - 18:54, 19 December 2018
- This includes target annotations and such, using the "800-lb-gorilla" format1 KB (204 words) - 21:08, 11 March 2020
- #x y z coords of target cys are the next 3 args #starting count from zero and target carbon is 53 KB (496 words) - 16:12, 14 February 2014
- ...nds that are too small (<200 amu) or too large (>500 amu) for a particular target. This routine can also be used to filter a database without performing any2 KB (225 words) - 23:40, 23 March 2016
- Protein Target Preparation2 KB (264 words) - 16:57, 28 August 2019
- ...elevant forms. It is available in subsets for general screening as well as target-, chemotype- and vendor-focused subsets. ZINC is free for everyone to use ZINC was originally designed for target based virtual screening (docking), and this remains its primary focus. Howe8 KB (1,258 words) - 23:54, 4 January 2019
- TARGET.TARGET_NAME, TARGET.SWISSPROT,2 KB (287 words) - 17:02, 18 March 2014
- 4. Charge axis. Depending on the target, you may have good reasons to exclude one or more charges from the popup.2 KB (259 words) - 20:04, 11 June 2015
- You will get a confirmation page showing that the target has been looked up correctly at the PDB. To proceed, click on "DOCK". Writ2 KB (302 words) - 02:22, 11 January 2019
- - '''uniprot''': categorized by target uniprot id2 KB (265 words) - 14:46, 21 March 2014
- * target affinitites of compounds, 10uM or better2 KB (288 words) - 14:50, 21 June 2015
- * chembl20, all cmpds also target free2 KB (224 words) - 23:50, 12 February 2016
- ...cules. The tool creates analogs through interchanging the substructures of target molecules through Bioisosteric transformations. Bioisosteres are molecular2 KB (337 words) - 18:48, 4 November 2022
- * 7. There are four target IDs in ChEMBL that have a NULL description. That would seem to be wrong, bu ...ta. These do not have specific targets, and so, cannot be given a specific Target ID (TID). 22226 and 22228 are 'Unchecked' and 'Unknown', respectively, and5 KB (737 words) - 14:46, 21 March 2014
- ...don't really care about properties, drug-likeness etc. So just go to your target on ChEMBL, grab the version with the highest number of compounds, and click2 KB (358 words) - 20:10, 22 September 2023
- #Flag to use critical point sphere labeling to target orientations to particular spheres3 KB (357 words) - 18:05, 15 February 2014
- ...org/targets.txt:target.uniprot?structure.contains=C(=O)[ND2][OD1]&distinct=target.uniprot&count=all World drugs with no gene target annotated and no SEA prediction18 KB (2,725 words) - 21:41, 29 October 2019
- ...elevant forms. It is available in subsets for general screening as well as target-, chemotype- and vendor-focused subsets. ZINC is free for everyone to use ZINC was originally designed for target based virtual screening (docking), and this remains its primary focus. Howe11 KB (1,604 words) - 23:52, 10 January 2019
- fragment (query and target must have same heavy atom network for matching, all features otherwise trea If y, generic tautomer of query and target used in search.5 KB (681 words) - 17:01, 18 March 2014
- 1. I made it so you can target regular db2.gz files instead of db2.tgz packages2 KB (339 words) - 19:38, 25 July 2022
- * Step 1. The target molecule is retrosynthesized through standard, robust reactions to separate2 KB (346 words) - 18:46, 4 November 2022
- * Step 1. The target molecule is retrosynthesized through standard, robust reactions to separate2 KB (346 words) - 18:34, 21 March 2023
- If you are a biologist or medicinal chemist, seeking new compounds for your target, you can search the libraries in 2D using Smallworld [[CC:Smallworld]] and2 KB (326 words) - 19:18, 20 September 2023
- ...|Search for Your Molecules in ZINC Using the UNIPROT Ascension ID for Your Target, for example OPRM1 for the Mu Receptor]]3 KB (480 words) - 18:49, 15 March 2019
- | [[SEA]] || Similarity Ensemble Approach || Drug repurposing, target ID3 KB (419 words) - 05:11, 3 June 2015
- set target = '*.smi' foreach i ($target)12 KB (1,637 words) - 23:38, 1 May 2024
- ...t should I do if DOCK Blaster has made completely wrong suggestions for my target? == ...8% of eligible targets. Thus there is a rather high probability that your target is not among the successful ones. Finally, it is important to remain skept9 KB (1,448 words) - 22:06, 5 April 2013
- * [[Protein Target Preparation]] - only beblasti and very basic blastermaster commands * [[Protein Target Preparation Updated]] - provides an explanation of what happens during Blas6 KB (844 words) - 17:03, 27 July 2021
- ...ght mouse clicking and selecting "save link as". If you are using your own target, you must prepare the files yourself (see [[DOCK Blaster:Input Preparation ** a. In the "Target" field, select the receptor, rec.pdb.10 KB (1,582 words) - 03:23, 12 March 2014
- ...ght mouse clicking and selecting "save link as". If you are using your own target, you must prepare the files yourself (see [[DOCK Blaster:Input Preparation ** a. In the "Target" field, select the receptor, rec.pdb.10 KB (1,582 words) - 03:23, 12 March 2014
- ...ght mouse clicking and selecting "save link as". If you are using your own target, you must prepare the files yourself (see [[DOCK Blaster:Input Preparation ** a. In the "Target" field, select the receptor, rec.pdb.10 KB (1,582 words) - 03:23, 12 March 2014
- ...ght mouse clicking and selecting "save link as". If you are using your own target, you must prepare the files yourself (see [[DOCK Blaster:Input Preparation ** a. In the "Target" field, select the receptor, rec.pdb.10 KB (1,582 words) - 03:24, 12 March 2014
- ...ght mouse clicking and selecting "save link as". If you are using your own target, you must prepare the files yourself (see [[DOCK Blaster:Input Preparation ** a. In the "Target" field, select the receptor, rec.pdb.10 KB (1,582 words) - 03:24, 12 March 2014
- ...e the :, no spaces) in the quick search bar are zinc, cas, smiles, drug, target, catalog and vendor. See the [[QSB]] article for examples. target.code=drd2-1-e3 KB (433 words) - 21:34, 28 December 2018
- ...information, this makes it easy to shop for compounds. Use the Search->by Target menu item.2 KB (375 words) - 23:15, 4 January 2019
- On Target Prep page clicked Reload Page button got "we have no idea what we were aske2 KB (435 words) - 20:25, 8 October 2012
- ...a pipeline with several steps. The time each step takes will depend on the target, any ligands you supply, and of course competition from other users for the3 KB (444 words) - 05:22, 13 March 2014
- ...lation should take between 15 and 30 minutes, but this will depend on your target and the load on our servers. If the preliminary calculations complete and a3 KB (449 words) - 20:02, 8 October 2012
- [[Category:Off target effects]]3 KB (439 words) - 06:42, 13 March 2014
- * move all files to the target platform3 KB (413 words) - 17:06, 8 April 2023
- | [[SEA]] || Similarity Ensemble Approach || Drug repurposing, target identification, phenotypic screening. [https://sea.bkslab.org/ sea.bkslab.o4 KB (494 words) - 20:17, 14 May 2024
- ...ds and their affinities against 102 targets, an average of 224 ligands per target. ! scope="row" | Number of ligands per target12 KB (1,955 words) - 20:35, 4 January 2019
- Table 3 - Gene Target Classes4 KB (836 words) - 23:50, 1 October 2015
- target="*.smi" for j in $target16 KB (2,279 words) - 18:01, 2 May 2024
- #target clustering3 KB (408 words) - 23:23, 4 January 2019
- ...ptors by clicking Receptors > Structure-based alignments and entering your target GPCR and your favorite template. (This can also be done via the API.) These ...d consequently are slightly more difficult to align correctly, but if your target sequence has these features, a candidate alignment should be viewed with sk12 KB (1,840 words) - 01:13, 1 June 2017
- In a busy instance, a few event loops runs will cause commands to target a few thousand of pages, causing the copy on write of almost the whole proc4 KB (577 words) - 17:34, 11 October 2019