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RAG: RNAAsGraphs database–concepts, analysis, and features
 Bioinformatics
, 2004
"... Motivation: Understanding RNA’s structural diversity is vital for identifying novel RNA structures and pursuing RNA genomics initiatives. By classifying RNA secondary motifs based on correlations between conserved RNA secondary structures and functional properties, we offer an avenue for predicting ..."
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Cited by 14 (5 self)
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Motivation: Understanding RNA’s structural diversity is vital for identifying novel RNA structures and pursuing RNA genomics initiatives. By classifying RNA secondary motifs based on correlations between conserved RNA secondary structures and functional properties, we offer an avenue for predicting novel motifs. Although several RNA databases exist, no comprehensive schemes are available for cataloguing the range and diversity of RNA’s structural repertoire. Results: Our RNAAsGraphs (RAG) database describes and ranks all mathematically possible (including existing and candidate) RNA secondary motifs on the basis of graphical enumeration techniques. We represent RNA secondary structures as twodimensional graphs (networks), specifying the connectivity between RNA secondary structural elements, such as loops, bulges, stems and junctions. We archive RNA tree motifs as ‘tree graphs ’ and other RNAs, including pseudoknots, as general ‘dual graphs’. All RNA motifs are catalogued by graph vertex number (a measure of sequence length) and ranked by topological complexity. The RAG inventory immediately suggests candidates for novel RNA motifs, either naturally occurring or synthetic, and thereby might stimulate the prediction and design of novel RNA motifs. Availability: The database is accessible on the web at
Randomly Sampling Molecules
 SIAM Journal on Computing
, 1996
"... We give the first polynomialtime algorithm for the following problem: Given a degree sequence in which each degree is bounded from above by a constant, select, uniformly at random, an unlabelled connected multigraph with the given degree sequence. We also give the first polynomialtime algorithm ..."
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Cited by 10 (2 self)
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We give the first polynomialtime algorithm for the following problem: Given a degree sequence in which each degree is bounded from above by a constant, select, uniformly at random, an unlabelled connected multigraph with the given degree sequence. We also give the first polynomialtime algorithm for the following related problem: Given a molecular formula, select, uniformly at random, a structural isomer having the given formula.
MOLGEN–CID, A Canonizer for Molecules and Graphs Accessible through the Internet
 J. Chem. Inf. Comput. Sci
, 2004
"... The MOLGEN Chemical Identifier MOLGENCID is a software module freely accessible via the Internet. For a molecule or graph entered in molfile format it produces, by a canonical renumbering procedure, a canonical molfile and a unique character string that is easily compared by computer to a similar s ..."
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Cited by 8 (7 self)
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The MOLGEN Chemical Identifier MOLGENCID is a software module freely accessible via the Internet. For a molecule or graph entered in molfile format it produces, by a canonical renumbering procedure, a canonical molfile and a unique character string that is easily compared by computer to a similar string. The mode of operation of MOLGENCID is detailed and visualized with examples.
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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Cited by 6 (4 self)
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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...
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