Molecular Analysis Pro^TM

• Now at version 3.2
• Developed by Norgwyn Montgomery Software Inc.
• Published by ChemSW
• Lead Programmer: James A. Quinn
• PLS routines: William Dunn III

QSAR (quantitative structure activity relationships) and QSPR (quantitative structure property relationships) study relationships between useful molecular properties (like ability to control a human disease or lubricate a piston) and the underlying chemical and physical properties which may enhance or limit the desired property.  Molecular Analysis Pro has three main features that aid in the discovery of these relationships:

• calculates molecular properties from structure
• contains statistical and graphing tools for analyzing data
• data base storage, retrieval and manipulation capacity

Program overview

• Limited data base capabilities

• Save/retrieve data bases of structures and properties of up to 3000 molecules, including 7 string fields and 72 floating point numeric fields.
• Sort/subset data by values.
• View record by record or as a table of data.
• Input/output data as ASCII comma separated value files (can be read by Microsoft EXCEL, ACCESS and most statistical packages) or as MDL SD Files (accessible by other Chemistry software including CHEMFINDER Ask TWC BioSearch for more CHEMFINDER information).
• Cut and paste records or fields via the clipboard

• Statistical analysis: Multiple linear regression, Partial least squares regression, Principle components analysis. MLR and PCA limited to 30 variables, PLS limited by memory and capable of handling multiple x and y.  Additional statistics: simple correlation, analysis of components of variance (complete block design only), simple statistics (mean, range etc.)
• Charting and graphing: x-y plots (many options), 3-D surface plots, contour maps, rotatable 3-D dot plots, bar charts
• Calculates about 50 molecular properties from structure
• Add substituent parameters (pi, MR, sterimol, sigma) to the data base from a file of literature values
• Will determine best replacements for a component of a mixture, based on similarity of physical properties
• Has a unique algorithm for creating models of physical properties from the atomic properties of molecules
• Displays structures (wire frame, ball and stick, spheres, plus connectivity to CHEMSITE's rendering capabilities)
• Comes with a data base of over 300 solvents, including many values from the literature as well as calculated fields
• Requires a companion program capable of creating new structures such as Molecular Modeling Pro or CHEMSITE.
• Molecular Modeling Pro is not required, but has additional data base creation tools, a structure editor and additional physical property calculations

New in version 3.2

• Cut and paste MDL Molfiles with the clipboard
• Create new data base entries by pasting MDL Molfile over the clipboard from CHEMSITE, Molecular Modeling Pro or Chemistry 4-D Draw
• Calculates about 50 molecular properties from structure
• Automated data base creation by importing MDL Molfiles, MACROMODEL files or Brookhaven protein data base files.  Whole directories of MDL Molfiles may be imported and physical properties calculated for them on the fly.
• "Quick" MM2 minimization of structures

• Multiple linear regression analysis output
• Partial least squares regression output
• Brute force regression using PLS
• X-Y plot
• 3-D surface plot
• Replacement of chloroform in a mixture

• molecular weight
• chemical formula
• SMILES notation
• van der Waals volume and surface area (method of A. Bondi, J. Phys. Chem. 68:441, 1964)
• length, width and depth along the x, y and z axes
• log Kow (octanol water partition coefficient, method of Crippen and Ghose, V.N. Viswanadhan, A.K. Ghose, G.R. Revankar and R.K. Robins, 1988, J. Chem. Inf. Comput. Sci., 29: 163-172)
• MR (molar refractivity, method of Crippen and Ghose, see reference above)
• HLB (hydrophilic lipophilic balance, MMP method)
• water solubility (G. Klopman, S. Wang and D.M. Balthasar, J. Chem. Inf. Comput. Sci. 32:474-482 (1992))
• percent hydrophilic surface area (MMP method)
• 3-D solubility parameters (i.e., dispersion, polarity, hydrogen bonding and the solubility parameter using van Krevelen's method, Properties of Polymers, 3rd edition, Elsevier)
• dipole moment (from modified DelRe charges)
• hydrogen bond acceptor and donor values (MMP method)
• connectivity indices 0-4, valence indices 0-4, kappa shape index 2   (method of Randic, Kier and Hall, L.B. Kier, L.H. Hall, W.J. Murray and M. Randic, J. Pharmaceutical Sci. 64: 1971-1974 (1975); W.J. Murray and L.B. Kier, J. Med. Chem. 19: 573-578 (1976); L.B. Kier, Quant. Struct.-Act. Relat. 4: 109-116 (1985); L.B. Kier and L.H. Hall, Molecular Connectivity in Chemistry and Drug Res., Academic, New York, 1976)
• thermodynamic properties including boiling point, vapor pressure, enthalpy of formation, Gibbs free energy of formation, heat capacity and several more (methods of Joback and Reid(K.G. Joback and R.C. Reid, Chem. Eng. Comm. 57:233-243 (1987), with some additional methods from S. Yalkowsky and collaborators, P. Myrdal, S. Yalkowsky,  Ind. Eng. Chem. Res. 36: 2494-99 (1997))
• substituent parameters: pi, MR, sigma para, sigma meta, sigma star, sterimol (B1, B5, L1)(values mainly from C. Hansch and A. Leo, Substituent Constants for Correlation Analysis in Chemistry and Biology by C. Hansch and A. Leo (1979), Wiley and Sons)

Looking for databases for Molecular Modeling Pro and Molecular Analysis Pro?
Check out our Chemical Structure and Information Databases.

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