Advanced Molecule Search

Advanced Molecule Search

Advanced search supports searching for molecules based on complex criteria.

1. Tag-Based Search (type=tags)

Search molecules based on the following tag types:

• dataSource: Search by collection title

  • Example: type=tags, tagType=dataSource, query=collection_name

• organisms: Search by organism names (comma-separated)

  • Example: type=tags, tagType=organisms, query=organism_name1,organism_name2

• citations: Search by DOI or title (comma-separated)

  • Example: type=tags, tagType=citations, query=doi1,doi2,title1,title2

2. Filter-Based Search (type=filters)

Molecular Properties

• tac: Total Atom Count (1-1071)
• hac: Heavy Atom Count (0-551)
• mw: Molecular Weight (5.01-7860.71)
• emw: Exact Molecular Weight (1.00728-7855.66038)
• mrc: Number of Minimal Rings (0-51)
• vdwv: Van der Walls Volume (10.14-5177.31)
• fc: Formal Charge (-8 to 7)

Chemical Properties

• alogp: ALogP (-82.67 to 67.03)
• topopsa: Topological Polar Surface Area (0.00-3453.72)
• fcsp3: Fraction CSP3 (0.00-1.00)
• np: NP Likeness (-3.53 to 4.12)
• qed: QED Drug Likeliness (0.00-0.95)

Structural Features

• rbc: Rotatable Bond Count (0-224)
• arc: Aromatic Rings Count (0-31)
• hba: Hydrogen Bond Acceptors (0-191)
• hbd: Hydrogen Bond Donors (0-116)

Lipinski Parameters

• lhba: Lipinski H-Bond Acceptors (0-191)
• lhbd: Lipinski H-Bond Donors (0-116)
• lro5v: Lipinski Rule of 5 Violations (0-4)

Sugar-Related Properties

• cs: Contains Sugar (true/false)
• crs: Contains Ring Sugars (true/false)
• cls: Contains Linear Sugars (true/false)

Classyfire Classifications

• class: Chemical Class
  • Example: 1,2-diaryl-2-propen-1-ols
• subclass: Chemical Sub Class
  • Example: 1,1'-azonaphthalenes
• superclass: Chemical Super Class
  • Example: Acetylides
• parent: Direct Parent Classification
  • Example: 1,1'-azonaphthalenes

Natural Product Classifications

• np_pathway: NP Classifier Pathway
  • Example: Amino acids and Peptides
• np_superclass: NP Classifier Superclass
  • Example: Aminosugars and aminoglycosides
• np_class: NP Classifier Class
  • Example: 2-arylbenzofurans
• np_glycoside: NP Classifier Is Glycoside (true/false)

Filter Query Examples

• Range query:

  type=filters&q=tac:4..6
  

• Boolean query:

  type=filters&q=cs:true
  

• Classification query:

  type=filters&q=class:1,2-diaryl-2-propen-1-ols
  

• Multiple conditions:

  type=filters&q=tac:4..6 mw:100..200
  

• Complex query with OR:

  type=filters&q=tac:4..6 cs:true OR mw:100..200
  

3. Basic Search (type not specified)

Search molecules by name, SMILES, InChI, or InChI Key.

• Simply provide the search term in the query parameter
• Example: query=caffeine