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Collaborative filtering on a family of biological targets
 J. Chem. Inf. Model
"... Supporting Information Links to the 3 articles that cite this article, as of the time of this article download Access to high resolution figures Links to articles and content related to this article Copyright permission to reproduce figures and/or text from this article ..."
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Supporting Information Links to the 3 articles that cite this article, as of the time of this article download Access to high resolution figures Links to articles and content related to this article Copyright permission to reproduce figures and/or text from this article
MOLecular Structure GENeration with MOLGEN, new features and future developments
 Fresenius J. Anal. Chem
, 1997
"... MOLGEN is a computer program system which is designed for generating molecular graphs fast, redundancy free and exhaustively. In the present paper we describe its basic features, new features of the current release MOLGEN 3.5, and future developments which provide considerable improvements and ex ..."
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MOLGEN is a computer program system which is designed for generating molecular graphs fast, redundancy free and exhaustively. In the present paper we describe its basic features, new features of the current release MOLGEN 3.5, and future developments which provide considerable improvements and extensions. 1 Introduction MOLGEN [17] is a generator for molecular graphs (=connectivity isomers or constitutional formulae) allowing to generate all isomers that correspond to a given molecular formula and (optional) further conditions like prescribed and forbidden substructures, ring sizes etc. The input consists of ffl the empirical formula, together with ffl an optional list of macroatoms, which means prescribed substructures that must not overlap, ffl an optional goodlist, that consists of prescribed substructures which may overlap, ffl an optional badlist, containing forbidden substructures, ffl an optional interval for the minimal and maximal size of rings, ffl an optional num...
Building–Block Computation of the Ivanciuc–Balaban Indices for the Virtual Screening
 of Combinatorial Libraries, Internet
"... Motivation. The discovery of drug leads is significantly accelerated by in silico screening of molecular libraries, that starts from a collection of chemical compounds with a high structural diversity and selects molecules according to their similarity toward specific collections of active compounds ..."
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Motivation. The discovery of drug leads is significantly accelerated by in silico screening of molecular libraries, that starts from a collection of chemical compounds with a high structural diversity and selects molecules according to their similarity toward specific collections of active compounds. In this process, the molecular similarity/diversity and the drug–like character are characterized with structural descriptors, such as structure keys, fingerprints, graph invariants and various topological indices computed from atomic connectivity or molecular matrices. Method. In this paper we present an efficient algorithm for the computation of the Ivanciuc–Balaban (IB) structural descriptors for large combinatorial libraries using only molecular graph descriptors of the building blocks. The procedure is developed for vertex – and edge–weighted molecular graphs representing organic
Cluj matrix invariants
 J. Chem. Inf. Comput. Sci
, 1997
"... The newly proposed matrix, CJu (unsymmetric Cluj matrix) is examplified for cyclecontaining structures. Its relation with the matrix SZu (unsymmetric Szeged matrix) is discussed both as definition and related indices. The derived "Cluj " numbers are compared to the Wiener matrix and Szeg ..."
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The newly proposed matrix, CJu (unsymmetric Cluj matrix) is examplified for cyclecontaining structures. Its relation with the matrix SZu (unsymmetric Szeged matrix) is discussed both as definition and related indices. The derived "Cluj " numbers are compared to the Wiener matrix and Szeged matrixderived numbers and tested for discriminating and correlating ability on selected sets of graphs. Motto: The existence of a nation is not discussed but affirmed! (I.Ratiu)
Development of binary classification of structural chromosome aberrations for a diverse set of organic compounds from molecular structure
, 2003
"... Classification models are generated to predict in vitro cytogenetic results for a diverse set of 383 organic compounds. Both knearest neighbor and support vector machine models are developed. They are based on calculated molecular structure descriptors. Endpoints used are the labels clastogenic or ..."
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Classification models are generated to predict in vitro cytogenetic results for a diverse set of 383 organic compounds. Both knearest neighbor and support vector machine models are developed. They are based on calculated molecular structure descriptors. Endpoints used are the labels clastogenic or nonclastogenic according to an in vitro chromosomal aberration assay with Chinese hamster lung cells. Compounds that were tested with both a 24 and 48 h exposure are included. Each compound is represented by calculated molecular structure descriptors encoding the topological, electronic, geometrical, or polar surface area aspects of the structure. Subsets of informative descriptors are identified with genetic algorithm feature selection coupled to the appropriate classification algorithm. The overall classification success rate for a knearest neighbor classifier built with just six topological descriptors is 81.2 % for the training set and 86.5 % for an external prediction set. The overall classification success rate for a threedescriptor support vector machine model is 99.7 % for the training set, 92.1 % for the crossvalidation set, and 83.8 % for an external prediction set.
Evolution of Metabolic Networks A Computational Framework
"... Background: The metabolic architectures of extant organisms share many key pathways such as the citric acid cycle, glycolysis, or the biosynthesis of most amino acids. Several competing hypotheses for the evolutionary mechanisms that shape metabolic networks have been discussed in the literature, ea ..."
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Background: The metabolic architectures of extant organisms share many key pathways such as the citric acid cycle, glycolysis, or the biosynthesis of most amino acids. Several competing hypotheses for the evolutionary mechanisms that shape metabolic networks have been discussed in the literature, each of which finds support from comparative analysis of extant genomes. Alternatively, the principles of metabolic evolution can be studied by direct computer simulation. This requires, however, an explicit implementation of all pertinent components: a universe of chemical reaction upon which the metabolism is built, an explicit representation of the enzymes that implement the metabolism, of a genetic system that encodes these enzymes, and of a fitness function that can be selected for. Results: We describe here a simulation environment that implements all these components in a simplified ways so that largescale evolutionary studies are feasible. We employ an artificial chemistry that views chemical reactions as graph rewriting operations and utilizes a toyversion of quantum chemistry to derive thermodynamic parameters.
Design of Topological Indices. Part 10. 1 Parameters Based on Electronegativity and Covalent Radius for the Computation of Molecular Graph Descriptors for HeteroatomContaining Molecules
, 1998
"... Two new approaches are presented for the calculation of atom and bond parameters for heteroatomcontaining molecules used in computing graph theoretic invariants. In the first approach, the atom and bond weights are computed on the basis of relative atomic electronegativity, using carbon as standard ..."
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Two new approaches are presented for the calculation of atom and bond parameters for heteroatomcontaining molecules used in computing graph theoretic invariants. In the first approach, the atom and bond weights are computed on the basis of relative atomic electronegativity, using carbon as standard. In the second system, the relative covalent radii are used to compute atom and bond weights, again with the carbon atom as standard. The new definition of the atom and bond parameters leads to a periodic variation versus the atomic number Z, with a more natural variation when compared with the parameters defined only by Z. The two approaches are used to define and compute topological indices based on graph distance. A quantitative structureproperty relationship study is reported for boiling points of 185 acyclic compounds with one or two oxygen or sulfur atoms (devoid of hydrogen bonding), in terms of four or five molecular descriptors.
Exploring the Limits of Graph Invariant and SpectrumBased Discrimination of (Sub)structures
 J. Chem. Inf. Comput. Sci. 2002
"... The limits of a recently proposed computer method for finding all distinct substructures of a chemical structure are systematically explored within comprehensive graph samples which serve as supersets of the graphs corresponding to saturated hydrocarbons, both acyclic (up to n = 20) and (poly)cyclic ..."
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The limits of a recently proposed computer method for finding all distinct substructures of a chemical structure are systematically explored within comprehensive graph samples which serve as supersets of the graphs corresponding to saturated hydrocarbons, both acyclic (up to n = 20) and (poly)cyclic (up to n = 10). Several pairs of smallest graphs and compounds are identified that cannot be distinguished using selected combinations of invariants such as combinations of Balaban’s index J and graph matrix eigenvalues. As the most important result, it can now be stated that the computer program NIMSG, using J and distance eigenvalues, is safe within the domain of mono through tetracyclic saturated hydrocarbon substructures up to n = 10 (oligocyclic decanes) and of all acyclic alkane substructures up to n = 19 (nonadecanes), i.e. it will not miss any of these substructures. For the regions surrounding this safe domain, upper limits are found for the numbers of substructures that may be lost in the worst case, and these are low. This taken together means that the computer program can be reasonably employed in chemistry whenever one is interested in finding the saturated hydrocarbon substructures. As to unsaturated and heteroatom containing substructures, there are reasons to conjecture that the method’s resolving power for them is similar. 1
Evaluation in Quantitative Structure–Property Relationship Models of Structural Descriptors Derived from Information–Theory Operators
 J. Chem. Inf. Comput. Sci
"... 252 BioChem Press ..."
How Good Can the Characteristic Polynomial Be for Correlations?
, 2007
"... Abstract: The aim of this study was to investigate the characteristic polynomials resulting from the molecular graphs used as molecular descriptors in the characterization of the properties of chemical compounds. A formal calculus method is proposed in order to identify the value of the characterist ..."
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Abstract: The aim of this study was to investigate the characteristic polynomials resulting from the molecular graphs used as molecular descriptors in the characterization of the properties of chemical compounds. A formal calculus method is proposed in order to identify the value of the characteristic polynomial parameters for which the extremum values of the squared correlation coefficient are obtained in univariate regression models. The developed calculation algorithm was applied to a sample of nonane isomers. The obtained results revealed that the proposed method produced an accurate and unique solution for the best relationship between the characteristic polynomial as molecular descriptor and the property of interest.