Computable molecular descriptors

P. S., Strategies toward predicting peptide cellular permeability from computed molecular descriptors, J. Pept. Res., 1999, 53, 355-369. 

A molecular field involves mapping the chemical forces between an interacting partner and a target (macro)molecule. As the information contained in 3D molecular fields is related to the interacting molecular partners, the amount of information in molecular interaction fields (MIFs) is in general superior to other mono-dimensionally or bi-dimensionally computed molecular descriptors. 

Basak, S. C., Mills, D., Gute, B. D., Hawkins, D. M. Predicting mutagenicity of congeneric and diverse sets of chemicals using computed molecular descriptors ... 

Chen, I.J., Taneja, R., Yin, D., Seo, P.R., Young, D., MacKerell, A.D. and Polli, J.E. (2006) Chemical substituent effect on pyridine permeability and mechanistic insight from computational molecular descriptors. Molecular Pharmacology, 3, 745-755. 

Theoretical molecular descriptors cover much broader varieties and usually are more readily available even though the complexity of their computational procedures may vary widely. Major classes of computed molecular descriptors include the following ... 

A quantitative structure-property relationship (QSPR) is a correlation between a property Yand one or several (m) computable molecular descriptors, Xi, X2,..., Xm ... 

Computable molecular descriptors differ from experimentally derived properties in two important ways ... 

Computable molecular descriptors that occur most frequently in QSPRs in this book are explained in Chapter 2. QSPRs and their statistical parameters are presented in the same way as shown for QPPRs in Section 1.4. Often, QSPR studies apply a set of molecular descriptors to compare their significance for the particular correlation. In this book we present only the most significant QSPRs as judged in the source or by the authors. 

Computable molecular descriptors have also been introduced in GCMs. The model then becomes... 

Since the first analysis by Hansch two significant developments have been made. The first is that a wide range of easily computable molecular descriptors are now available and the second is that many sophisticated techniques have emerged that are a significant improvement over the original linear regression... 

MODEL Molecular Descriptor Lab (MODEL) (http //jing.cz3.nus.edu.sg/ cgi-bin/model/model.cgi) is a free Web-based server for computing a comprehensive set of 3778 molecular descriptors, which can be divided into 6 classes constitutional descriptors, electronic descriptors, physical chemistry properties, topological indexes, geometrical molecular descriptors, and quantum chemistry descriptors [73], Compounds can be provided to the server in various molecular formats such as PDB, MDL, MOL2, and COR, and the computed molecular descriptors are displayed in a few seconds or less. Cross-links to the relevant sections of the reference manual page are also provided for some of the descriptors and descriptor classes. 

Goodwin JT, Mao B, Vidmar TJ, Conradi RA, and Burton PS. Strategies Toward Predicting Peptide Cellular Permeability from Computed Molecular Descriptors./Pejlihde 1999 53 355-369. 

Katritzky, A.R., Pacureanu, L., Dobchev, D. and Karelson, M. (2007) QSPR study of critical micelle concentration of anionic surfactants using computational molecular descriptors. /. Chem. Inf. Model, 47, 782-793. 

Rg. 6-10 Mapping chemical space [76]. Principle component models of chemical space are shown for 480 small molecules analyzed using 24 computed molecular descriptors and 60 measured phenotypic descriptors derived from a cell-based assay of cell proliferation. By considering the elements of S as coordinates, small molecules can be modeled as vectors,... 

Given a multidimensional matrix of data derived from chemical-genetic screens and computed molecular descriptors (Fig. 6-10), meaningful visual... 

Fig. 6-13 Overview of chemical space. On the left, chemicals are positioned in space using computed molecular descriptors. On the right chemicals are positioned in space using measured phenotypic descriptors of biological activity.

Another report on ion-pair chromatography, where computed molecular descriptors from molecular modeling were nicely correlated with experimental separation factors, was published by Karlsson, Luthman, Pettersson and Hacksell [81]. They examined factors responsible for separation of aminotetralins on achiral stationary phases in the presence of the chiral additive N-benzyloxycarbonylglycyl-L-proline (L-ZGP), a protected peptide derivative. 

Step 13 Compute molecular descriptors for screening by evaluating the scores DragLike, Lead Like, Progressive DragLike, Progressive LeadLike (DL, LL, PDL, PLL), toxicophore-based scores, pharmacophore-based scores, etc. as filters... 

Kiialj, R., Takahata, Y., Ferreira, M. M. C. (2003). QSAR of progestagens use of a priori and computed molecular descriptors and molecular graphics. QSAR Comb. Sci. 22(4), 430-448. 

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