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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...
Fast Similarity Search in ThreeDimensional Structure Databases
 Journal of Chemical Information and Computer Sciences
, 2000
"... this paper we study the similarity search problem and a class of related queries. ..."
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Cited by 5 (1 self)
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this paper we study the similarity search problem and a class of related queries.
Use of Statistical and Neural Net Methods in Predicting Toxicity of Chemicals: A Hierarchical QSAR Approach
 Predictive Toxicology of Chemicals: Experiences and Impacts of AI Tools
, 1999
"... A contemporary trend in computational toxicology is the prediction of toxicity endpoints and toxic modes of action of chemicals from parameters that can be calculated directly from their molecular structure. Topological, geometrical, substructural, and quantum chemical parameters fall into this ..."
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A contemporary trend in computational toxicology is the prediction of toxicity endpoints and toxic modes of action of chemicals from parameters that can be calculated directly from their molecular structure. Topological, geometrical, substructural, and quantum chemical parameters fall into this category. We have been involved in the development of a new hierarchical quantitative structureactivity relationship (QSAR) approach in predicting physicochemical, biomedicinal and toxicological properties of various sets of chemicals. This approach uses increasingly more complex molecular descriptors for model building in a graduated manner. In this paper we will apply statistical and neural net methods in the development of QSAR models for predicting toxicity of chemicals using topostructural, topochemical, geometrical, and quantum chemical indices. The utility and limitations of the approach will be discussed. Introduction In 1998 the number of chemicals registered with the...
Hazard assessment modeling: An evolutionary ensemble approach
 Proceedings of the Genetic and Evolutionary Computation Conference: GECCO1999
, 1999
"... This paper presents a novel and effective genetic algorithm approach for generating computational models for hazard assessment. With millions of proposed chemicals being registered each year, it is impossible to come even remotely close to completing the battery of tests needed for the proper unders ..."
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This paper presents a novel and effective genetic algorithm approach for generating computational models for hazard assessment. With millions of proposed chemicals being registered each year, it is impossible to come even remotely close to completing the battery of tests needed for the proper understanding of the toxic e#ects of these chemicals. Computer models can give quick, cheap, and environmentally friendly hazard assessments of chemicals. Our approach works by first extracting a hierarchy of theoretical descriptors of the structure of a compound, then filtering these numerous descriptors with a genetic algorithm approach to ensemble feature selection. We tested the utility of our approach by modeling the acute aquatic toxicity (LC 50) of a congeneric set of 69 benzene derivatives. Our results demonstrate a very important point: that our method is able to accurately predict toxicity directly from structure.
Graph Theory. 1. Fragmentation of Structural Graphs
 Journal of Practices and Technologies
, 2002
"... The investigation of structural graphs has many fields of applications in engineering, especially in applied sciences like as applied chemistry and physics, computer sciences and automation, electronics and telecommunication. The main subject of the paper is to express fragmentation criteria in grap ..."
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The investigation of structural graphs has many fields of applications in engineering, especially in applied sciences like as applied chemistry and physics, computer sciences and automation, electronics and telecommunication. The main subject of the paper is to express fragmentation criteria in graph using a new method of investigation: terminal paths. Using terminal paths are defined most of the fragmentation criteria that are in use in molecular topology, but the fields of applications are more generally than that, as I mentioned before. Graphical examples of fragmentation are given for every fragmentation criteria. Note that all fragmentation is made with a computer program that implements a routine for every criterion.[1] A web routine for tracing all terminal paths in graph can be found at the address:
Characterization of Isospectral Graphs Using Graph Invariants and Derived Orthogonal Parameters
 J. Chem. Inf. Comput. Sci. 1998
"... from TIs have been used in discriminating a set of isospectral graphs. Results show that lower order connectivity and information theoretic TIs suffer from a high degree of redundancy, whereas higher order indices can characterize the graphs reasonably well. On the other hand, PCs derived from the T ..."
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from TIs have been used in discriminating a set of isospectral graphs. Results show that lower order connectivity and information theoretic TIs suffer from a high degree of redundancy, whereas higher order indices can characterize the graphs reasonably well. On the other hand, PCs derived from the TIs had no redundancy for the set of isospectral graphs studied. 1.
Mathematical Simulations in Combinatorial Chemistry
, 1996
"... A novel technique for chemical synthesis in drug research is combinatorial chemistry, where usually a set of buildingblock molecules is attached to a core structure in all the combinatorially possible ways. The resulting set of compounds (called a library) can then be systematically screened for a ..."
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A novel technique for chemical synthesis in drug research is combinatorial chemistry, where usually a set of buildingblock molecules is attached to a core structure in all the combinatorially possible ways. The resulting set of compounds (called a library) can then be systematically screened for a desired biological activity. In this paper we discuss ways and limits of a mathematical simulation of this procedure. At first, two methods for selecting the buildingblocks from a given structure pool are presented with the objective to obtain only dissilimar library entries. Next an algorithm is described for the exhaustive and redundancyfree generation of a combinatorial library, illustrated by a singlestep and a multicomponent reaction. Finally equations for the enumeration of the library sizes are derived and the limits of the virtual combinatorial chemistry, i.e. purely in computer and without experiment, are discussed. 1