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Schrödinger extension for KNIME Workbench version by Schrödinger

QikProp is a quick, accurate, easy-to-use absorption, distribution, metabolism, and excretion (ADME) prediction program designed by Professor William L. Jorgensen. QikProp predicts physically significant descriptors and pharmaceutically relevant properties of organic molecules, either individually or in batches.

In addition to predicting molecular properties, QikProp provides ranges for comparing a particular molecule’s properties with those of 95% of known drugs. QikProp also flags 30 types of reactive functional groups that may cause false positives in high-throughput screening (HTS) assays.

Backend implementation

qikprop is used to generate output in SD or Maestro format based on the input format

Properties/descriptors calculated by QikProp:
#stars Number of property or descriptor values that fall outside the 95% range of similar values for known drugs.
#amine Number of non-conjugated amine groups
#amidine Number of non-conjugated amine groups
#acid Number of carboxylic acid groups
#amide Number of non-conjugated amide groups.
#rotor Number of non-trivial (not CX3), non-hindered (not alkene, amide, small ring) rotatable bonds
#rtvFG Number of reactive functional groups
CNS Predicted central nervous system activity
mol_MW Molecular weight of the molecule
dipole Computed dipole moment of the molecule
SASA Total solvent accessible surface area (SASA) in square angstroms using a probe with a 1.4 Å radius
FOSA Hydrophobic component of the SASA (saturated carbon and attached hydrogen)
FISA Hydrophilic component of the SASA (SASA on N, O, and H on heteroatoms)
PISA π (carbon and attached hydrogen) component of the SASA
WPSA Weakly polar component of the SASA (halogens, P, and S)
volume Total solvent-accessible volume in cubic angstroms using a probe with a 1.4 Å radius
donorHB Estimated number of hydrogen bonds that would be donated by the solute to water molecules in an aqueous solution
accptHB Estimated number of hydrogen bonds that would be accepted by the solute from water molecules in an aqueous solution
dip^2/V Square of the dipole moment divided by the molecular volume
ACxDN^.5/SA Index of cohesive interaction in solids
glob Globularity descriptor
QPpolrz Predicted polarizability in cubic angstroms
QPlogPC16 Predicted hexadecane/gas partition coefficient
QPlogPoct Predicted octanol/gas partition coefficient
QPlogPw Predicted water/gas partition coefficient
QPlogPo/w Predicted octanol/water partition coefficient
QPlogS Predicted aqueous solubility
CIQPlogS Conformation-independent predicted aqueous solubility
QPlogHERG Predicted IC50 value for blockage of HERG K+ channels
QPPCaco Predicted apparent Caco-2 cell permeability in nm/sec
QPlogBB Predicted brain/blood partition coefficient
QPPMDCK Predicted apparent MDCK cell permeability in nm/sec
QPlogKp Predicted skin permeability
IP(eV) PM3 calculated ionization potential (negative of HOMO energy)
EA(eV) PM3 calculated electron affinity (negative of LUMO energy)
#metab Number of likely metabolic reactions
QPlogKhsa Prediction of binding to human serum albumin
HumanOralAbsorption Predicted qualitative human oral absorption
PercentHumanOralAbsorption Predicted human oral absorption on 0 to 100% scale
SAfluorine Solvent-accessible surface area of fluorine atoms
SAamideO Solvent-accessible surface area of amide oxygen atoms
PSA Van der Waals surface area of polar nitrogen and oxygen atoms
#NandO Number of nitrogen and oxygen atoms
RuleOfFive Number of violations of Lipinski’s rule of five
RuleOfThree Number of violations of Jorgensen’s rule of three
#ringatoms Number of atoms in a ring
#in34 Number of atoms in 3- or 4-membered rings
#in56 Number of atoms in 5- or 6-membered rings
#noncon number of ring atoms not able to form conjugated aromatic systems (e.g. sp3 C)
#nonHatm Number of heavy atoms (nonhydrogen atoms)
Note: More information are available in the Qikprop manual.


Column containing input structures
Select the column in the input data table that contains the input molecules.
Output Column Structure
Choose the output columns:

Input plus Output - The input columns are included in the output.

Output replaced within Input columns - The output columns are the same as the input, with the output structures replacing the input column selected

Output only - Only Output structures

Fast mode
Run QikProp in fast mode
Extract all QikProp properties
Extracts all properties generated to output table
Show program out and csv views
If selected, the second and third views will be generated. This is off by default and not recommended if processing large numbers of structures.

Input Ports

Input molecules (in SD or Maestro format)

Output Ports

Molecules with ADME properties (in SD or Maestro format, the same as the input type)


Log output of Qikprop
Log output of Qikprop
Out output of Qikprop
Out output of Qikprop
CSV output of Qikprop
CSV output of Qikprop

Best Friends (Incoming)

Best Friends (Outgoing)



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