Difference between revisions of "Pharmaceutical Compounds analysis"

From BioUML platform
Jump to: navigation, search
(Automatic synchronization with BioUML)
 
(Automatic synchronization with BioUML)
 
(One intermediate revision by one user not shown)
Line 9: Line 9:
  
 
==== Description ====
 
==== Description ====
Pharmaceutical Compounds analysis
+
This method seeks for the optimal combination of molecular targets among input genes that potentially interact with pharmaceutical compounds from a library of known drugs and biologically active chemical compounds predicted with the cheminformatics tool PASS.
  
 
==== Parameters: ====
 
==== Parameters: ====
Line 16: Line 16:
 
* '''Weight column''' (expert) – Genes<nowiki>'</nowiki> weight column name
 
* '''Weight column''' (expert) – Genes<nowiki>'</nowiki> weight column name
 
* '''Diseases names''' – Names of the diseases, all diseases will be considered if nothing is selected
 
* '''Diseases names''' – Names of the diseases, all diseases will be considered if nothing is selected
* '''Use known compounds''' – Flag to show that known compounds should be used.
 
 
* '''Minimal targets''' – Minimal targets linked with structure satisfying conditions
 
* '''Minimal targets''' – Minimal targets linked with structure satisfying conditions
 
* '''Use custom targets threshold''' – Flag to show that targets threshold is enabled. If disabled would be cut off if Pa<Pi
 
* '''Use custom targets threshold''' – Flag to show that targets threshold is enabled. If disabled would be cut off if Pa<Pi
Line 23: Line 22:
 
* '''Use custom diseases threshold''' – Flag to show that diseases threshold is enabled. If disabled would be cut off if Pa<Pi
 
* '''Use custom diseases threshold''' – Flag to show that diseases threshold is enabled. If disabled would be cut off if Pa<Pi
 
* '''Diseases threshold (Pb)''' – Threshold (Pb) to cut off structures with Pa<Pb for all effects which corresponds to selected diseases
 
* '''Diseases threshold (Pb)''' – Threshold (Pb) to cut off structures with Pa<Pb for all effects which corresponds to selected diseases
 +
* '''False positive target weight''' (expert) – Weight of false positive targets in target activity score formula. False positive targets are known targets of the drug that are not included in input targets list
 
* '''Output table with structures''' – Output table with structures
 
* '''Output table with structures''' – Output table with structures
 
* '''Output table with targets''' – Output table with targets
 
* '''Output table with targets''' – Output table with targets

Latest revision as of 18:15, 9 December 2020

Analysis title
Default-analysis-icon.png Pharmaceutical Compounds analysis
Provider
Biosoft
Class
PCAnalysis
Plugin
biouml.plugins.genomeenhancer (Genome Enhancer)

[edit] Description

This method seeks for the optimal combination of molecular targets among input genes that potentially interact with pharmaceutical compounds from a library of known drugs and biologically active chemical compounds predicted with the cheminformatics tool PASS.

[edit] Parameters:

  • Genes table – Path to table with genes
  • Weight column (expert) – Genes' weight column name
  • Diseases names – Names of the diseases, all diseases will be considered if nothing is selected
  • Minimal targets – Minimal targets linked with structure satisfying conditions
  • Use custom targets threshold – Flag to show that targets threshold is enabled. If disabled would be cut off if Pa<Pi
  • Targets threshold (Pm) – Threshold (Pm) to cut off targets with Pa<Pm
  • Toxicities threshold (Pt) – Threshold (Pt) to cut off structures with Pa>Pt for at least one toxicity
  • Use custom diseases threshold – Flag to show that diseases threshold is enabled. If disabled would be cut off if Pa<Pi
  • Diseases threshold (Pb) – Threshold (Pb) to cut off structures with Pa<Pb for all effects which corresponds to selected diseases
  • False positive target weight (expert) – Weight of false positive targets in target activity score formula. False positive targets are known targets of the drug that are not included in input targets list
  • Output table with structures – Output table with structures
  • Output table with targets – Output table with targets
Personal tools
Namespaces

Variants
Actions
BioUML platform
Community
Modelling
Analysis & Workflows
Collaborative research
Development
Virtual biology
Wiki
Toolbox