CODESSA

CODESSA (calculation of a series of difFerent descriptors including quantum chemical descriptors) Semichem Inc. - 7204 Mullen, Shawnee, KS 66216, USA http //www.semichem.com... 

CODESSA (we tested Version 2.6) stands for comprehensive descriptors for structural and statistical analysis. It is a conventional QSAR/QSPR program. 

CODESSA reads molecular structure files or output files created by other software packages as the starting point for QSAR analysis. It can import computational results from AMPAC, MOPAC, and Gaussian as well as structures in a number of common formats. 

CODESSA can compute or import over 500 molecular descriptors. These can be categorized into constitutional, topological, geometric, electrostatic, quantum chemical, and thermodynamic descriptors. There are automated procedures that will omit missing or bad descriptors. Alternatively, the user can manually define any subset of structures or descriptors to be used. 

The relevance of size-related properties of hERG-blocking molecules was also detected in a 2D QSAR model developed by Coi et al. [22] after the analysis of 82 compounds through the CODESSA method. These authors developed two multiparameter models with strong predictive properties, from which, besides the involvement of hydrophobic features, the importance of linearity as opposed to globularity of the hERG blockers emerged. 

Coi, A., Massarelli, I., Murgia, L., Saraceno, M., Calderone, V. and Bianucd, A.M. (2006) Prediction of hERG potassium channel affinity by the CODESSA approach. Bioorganic el Medicinal Chemistry Letters, 14, 3153-3159. 

Randic M, Pompe M (2001a) The variable connectivity index %f versus the traditional molecular descriptors A comparative study of against descriptors of CODESSA. J. Chem. Inf. Comput. Sci. 41 631-638. 

Katritzky AR, Lobanov VS, Karelson M (1994) CODESSA software. Copyright 1994, University of Florida. SemiChem, Inc, Shawnee, KS... 

CODESSA General property prediction group www.semichem.com/... 

CODESSA Constitutional, topological, geometrical, electrostatic, surface property, quantum chemical, and thermodynamic descriptors 1,500... 

Katritzky, A.R., Karelson, M., Petrukhin, R. 1994. The CODESS A PRO project Comprehensive descriptors for structural and statistical analysis. http //www.codessa-pro.com/manual/manual.htm. 

Nowadays, more than 4000 types of descriptors are known.17 There exist different ways to classify them. With respect to the type of molecular representation used for their calculations—chemical formula, molecular graph, or spatial positions of atoms—one speaks about ID, 2D, and 3D descriptors, respectively. Descriptors can be global (describing the molecule as a whole) and local (only selected parts are considered). One could distinguish information-based descriptors, which tend to code the information stored in molecular structures, and knowledge-based (or semiempir-ical) descriptors issued from the consideration of the mechanism of action. Most of those descriptors can be obtained with the DRAGON, CODESSA PRO, and ISIDA programs. 

CODESSA PRO Program, http //www.codessa-pro.com/manual/manual.htm, 2008. 

Chemical information can be expressed in a number of ways. Chemical descriptors are commonly used in QSAR. There are thousands of chemical descriptors possibly used in QSAR. Indeed, programs such as DRAGON and CODESSA, just to name a couple, can calculate thousands of parameters [7, 8]. Chemical descriptors have different complexities. Some of them do not require any information on the structure, such as molecular weight. Others refer to the bidimensional structure, such as the number of double bonds. While some others require tridimensional information, such as molecular volume. Chemical descriptors can be geometrical, topological, quantum-mechanical, electrostatical, etc. There are a few books describing chemical descriptors [7, 8],... 

A.R. Katritzky et al., CODESSA PRO. Comprehensive DEscriptors for Structural and Statistical Analysis, University of Florida, USA, 2001-2005. http //www.codessa-pro.com. Accessed June 2007... 

CODESSA Semichem Inc. www. semichem. com/codessa. html Topological, geometric, constitutional, thermodynamic, electrostatic, quantum mechanical descriptors... 

We have evaluated three different techniques to generate QSAR models, namely Comparative Molecular Field Analysis (CoMFA), Comprehensive Descriptors for Structural and Statistical Analysis (CODESSA), and Hologram QSAR (HQSAR). More specifically they were evaluated for their utility (predictivity, speed, accuracy, and reproducibility) to predict ER binding activity quantitatively (Tong et al., 1998 Shi et al., 2001). Common to the three QSAR methods is the... 

Katritsky, Lobanov, and Karelson correlated the boiling point, (K), for a set of 584 compounds with a very large set (>800) descriptors of various types, including many of those employed by Jurs and colleagues. Equation [47] regresses on eight descriptors. As before, QM descriptors were calculated with the AMI Hamiltonian and other calculations were done with CODESSA. 

Following a similar approach but using a smaller data set of 369 compounds, Ivanciuc et al. correlated their liquid viscosity (10 Pa s) at 298 K with a mixed set of descriptors to obtain Eq. [48]. This involves three QM descriptors, one topological, and one constitutional descriptor. The QM descriptors were calculated with the AMI Hamiltonian in AMPAC, and CODESSA was used to calculate the descriptors and perform the statistical analyses. The HDCA2 parameter is the same HBD charged surface area used in Eq. [46]. The maximum electrophilic reactivity index, Ep, for a carbon atom is defined by X/ lumo,/A lumo+ 10), with the summation over the valence AOs on a carbon atom in the LUMO. The maximum AO electronic population, Y, models the molecular nucleophilicity and is defined by... 

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