On-line WWW resources for Phys-Chem Property Calculations*
* this is a continuously updated version of resources published in: Tetko I.V. The WWW as a tool to obtain molecular parameters, Mini Rev Med Chem, 2003, 3(8), 809-20, article.
- Actelion developed OSIRIS property explore applet that draws chemical structures and simultaneously calculates on-the-fly various drug-relevant properties, using a fragment-based approach, whenever a structure is valid. The predicted values are shown both as numbers and are coded in colors. The applet predicts log P, solubility and drug-likeness, estimated as proportion of fragments in drugs and various commercially available chemicals.
- Advanced Chemistry Development provides free single-molecule calculations of log P, molar refractivity, molar volume, parachor, polarizability and a number of other molecular properties. The same company provides commercial services including calculation of different physicochemical properties such as log P, log D, aqueous solubility, pKa, etc.
- Computer Chemie Centrum, the University of Erlangen-Nuremberg provides on-line access to a large number of molecular, atomic and bond properties calculated by the Parameter Estimation for the Treatment of Reactivity Applications (PETRA) program. This program can be used to quantify heats of formation, bond dissociation energies, sigma/pi charge distribution, inductive, polarizability and resonance effects and delocalization energies. Another popular software developed by this group, CORINA, provides 2D => 3D conversion of molecules.
- ChemSilico provides on-line calculation of different physicochemical (aqueous solubility, log D, pKa) and biological parameters (blood-brain barrier partition, plasma protein binding, mutagenicity prediction). The site contains information with detailed statistics about performance of different prediction modules. A registration is required.
- Jenner Institute LogPCalc provides prediction of lipophilicity for proteins and converts sequence, ie. MAT to SMILES NC(CCSC)C(=O)NC(C)C(=O)NC(C(C)O)C(=O)O.
- Molinspiration Cheminformatics provides calculation of molecular physicochemical properties relevant to drug design, including log P, molecular polar surface area (PSA), drug likeness and others.
- Pharma Algorithms provides on-line calculation using ADME/Tox Web of a number of PhysChem (logP, TPSA), Solubility (logSw), Ionization (pKa), P-gp, Oral Bioavailability, Abraham's solvation parameters, human intestinal absorption, Caco-2 permeability, and other parameters. A registration is required.
- Pre-ADME calculates different molecular descriptors, lipophilicity, aqueous solubility, molecular refractivity, polarizability, water solvation free energy, drug-likeness and drug absorption data such as Caco-2, MDCK, BBB, HIA. The user can draw input structures using ACD Structure Drawing Applet (ACD/SDA, https://www.acdlabs.com/products/java/sda) or upload input file in "sdf" or "mol" file format. The use of this software requires membership.
- SPARC server facilitates chemical fate modeling and calculates pKa, boiling point, refractive index, polarizability, vapor pressure and aqueous solubility (two last parameters require melting point) and a number of other parameters. The user can also do kinetics and hydrolysis analysis. The server provides database search of pKa and physical property values.
- Syracuse Research Corporation provides on-line interface to the KOWWIN program to estimate lipophilicity of chemical compounds. The compounds can be submitted as SMILES or CAS RN. In addition to calculated values, this site also provides experimental log P values of compounds from the PHYSPROP database.
- Quantum Pharmaceutical provides on-line calculation of logP lipophilicity of chemical compounds. The compounds can be submitted in .hin, .sdf, .mol2, .pdb file formats.
- VCCLAB provides calculation of lipophilicity and aqueous solubility of chemicals and compares several algorithms. This site also performs on-line calculation of molecular descriptors using e-DRAGON using client-server interface to the DRAGON software of Prof. Todeschini.
Send an e-mail to Igor V. Tetko for a re-print of this article or to add a link with new WWW resources.