Paper Info
Title
TGSA-Flex: Extending the capabilities of the Topo-Geometrical Superposition Algorithm to handle flexible molecules.
Abstract
In this work, an extension of the already studied Topo-Geometrical Superposition Approach (TGSA) is presented. TGSA, a general-purpose, fast, automatic, and, user-intuitive, three-dimensional molecular alignment procedure, was originally designed to superpose rigid molecules simply based on atomic numbers, molecular coordinates, and connectivity. The algorithm is further developed to enable handling rotations around single bonds; in this way, common structural features, which were not properly aligned due to conformational causes, can be brought together, thus improving the molecular similarity picture of the final alignment. The Present procedure, implemented in Fortran 90 and named TGSA-Flex, is deeply detailed and tested over four molecular sets: amino acids, nordihydroguaiaretic acid (NDGA) derivatives, HIV-1 protease inhibitors, and 1-[2-hydroxyethoxy methyl]-6-(phenylthio)thymine (HEPT) derivatives. TGSA-Flex performance is evaluated by means of computational time, number of superposed atoms (also comparing it with respect to the rigid approach), and index of fit between the compared structures.
Year
DOI
Venue
2004
10.1002/jcc.10258
JOURNAL OF COMPUTATIONAL CHEMISTRY
Keywords
Field
DocType
molecular superposition,flexible alignment,flexibility,rotary bonds,Topo-Geometrical Approach,TGSA,computer program
Atomic number,Superposition principle,Computer science,Molecule,Computational chemistry,Fortran,Algorithm,Atom,FLEX,Computer program,Single bond
Journal
Volume
Issue
ISSN
25.0
2
0192-8651
Citations 
PageRank 
References 
5
0.45
20
Authors
2
Name
Order
Citations
PageRank
Xavier Gironés1618.17
Ramon Carbó-Dorca219928.14