Literature DB >> 1291629

A fast and efficient method for 2D and 3D molecular shape description.

G W Bemis1, I D Kuntz.   

Abstract

A new formalism for molecular shape description is described. The formalism, based on considering each molecule as a collection of its 3-atom submolecules, is applied to both the graph theory and geometrical coordinate representations of molecules. The timing results for shape description of several databases indicate that this new method is applicable to large databases. Furthermore, results from clustering a small database show good agreement with clustering results obtained by a distance-matching algorithm.

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Year:  1992        PMID： 1291629     DOI： 10.1007/bf00126218

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN： 0920-654X            Impact factor:   3.686


  20 in total

1.  On using the adjacency matrix power method for perception of symmetry and for isomorphism testing of highly intricate graphs.

Authors:  G Rücker; C Rücker
Journal:  J Chem Inf Comput Sci       Date:  1991-02

2.  Molecular structure matching by simulated annealing. IV. Classification of atom correspondences in sets of dissimilar molecules.

Authors:  M C Papadopoulos; P M Dean
Journal:  J Comput Aided Mol Des       Date:  1991-04       Impact factor: 3.686

3.  A method for automatic generation of novel chemical structures and its potential applications to drug discovery.

Authors:  R Nilakantan; N Bauman; R Venkataraghavan
Journal:  J Chem Inf Comput Sci       Date:  1991-11

4.  Molecular structure matching by simulated annealing. I. A comparison between different cooling schedules.

Authors:  M T Barakat; P M Dean
Journal:  J Comput Aided Mol Des       Date:  1990-09       Impact factor: 3.686

5.  Techniques for the calculation of three-dimensional structural similarity using inter-atomic distances.

Authors:  C A Pepperrell; P Willett
Journal:  J Comput Aided Mol Des       Date:  1991-10       Impact factor: 3.686

6.  Clustering a large number of compounds. 1. Establishing the method on an initial sample.

Authors:  L Hodes
Journal:  J Chem Inf Comput Sci       Date:  1989-05

7.  Docking flexible ligands to macromolecular receptors by molecular shape.

Authors:  R L DesJarlais; R P Sheridan; J S Dixon; I D Kuntz; R Venkataraghavan
Journal:  J Med Chem       Date:  1986-11       Impact factor: 7.446

8.  MENTHOR, a database system for the storage and retrieval of three-dimensional molecular structures and associated data searchable by substructural, biologic, physical, or geometric properties.

Authors:  Y C Martin; E B Danaher; C S May; D Weininger
Journal:  J Comput Aided Mol Des       Date:  1988-04       Impact factor: 3.686

9.  Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure.

Authors:  R L DesJarlais; R P Sheridan; G L Seibel; J S Dixon; I D Kuntz; R Venkataraghavan
Journal:  J Med Chem       Date:  1988-04       Impact factor: 7.446

10.  A geometric approach to macromolecule-ligand interactions.

Authors:  I D Kuntz; J M Blaney; S J Oatley; R Langridge; T E Ferrin
Journal:  J Mol Biol       Date:  1982-10-25       Impact factor: 5.469
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  10 in total

1.  Feature trees: a new molecular similarity measure based on tree matching.

Authors:  M Rarey; J S Dixon
Journal:  J Comput Aided Mol Des       Date:  1998-09       Impact factor: 3.686

2.  Molecular modeling of G-protein coupled receptor kinase 2: docking and biochemical evaluation of inhibitors.

Authors:  M U Kassack; P Högger; D A Gschwend; K Kameyama; T Haga; R C Graul; W Sadée
Journal:  AAPS PharmSci       Date:  2000

3.  New molecular shape descriptors: application in database screening.

Authors:  A C Good; T J Ewing; D A Gschwend; I D Kuntz
Journal:  J Comput Aided Mol Des       Date:  1995-02       Impact factor: 3.686

4.  Investigating the extension of pairwise distance pharmacophore measures to triplet-based descriptors.

Authors:  A C Good; I D Kuntz
Journal:  J Comput Aided Mol Des       Date:  1995-08       Impact factor: 3.686

5.  Spatial chemical distance based on atomic property fields.

Authors:  A V Grigoryan; I Kufareva; M Totrov; R A Abagyan
Journal:  J Comput Aided Mol Des       Date:  2010-03-13       Impact factor: 3.686

6.  Bile pigments as HIV-1 protease inhibitors and their effects on HIV-1 viral maturation and infectivity in vitro.

Authors:  F McPhee; P S Caldera; G W Bemis; A F McDonagh; I D Kuntz; C S Craik
Journal:  Biochem J       Date:  1996-12-01       Impact factor: 3.857

7.  IDSS: deformation invariant signatures for molecular shape comparison.

Authors:  Yu-Shen Liu; Yi Fang; Karthik Ramani
Journal:  BMC Bioinformatics       Date:  2009-05-22       Impact factor: 3.169

8.  3DMolNavi: a web-based retrieval and navigation tool for flexible molecular shape comparison.

Authors:  Yu-Shen Liu; Meng Wang; Jean-Claude Paul; Karthik Ramani
Journal:  BMC Bioinformatics       Date:  2012-05-14       Impact factor: 3.169

Review 9.  Advances in the Development of Shape Similarity Methods and Their Application in Drug Discovery.

Authors:  Ashutosh Kumar; Kam Y J Zhang
Journal:  Front Chem       Date:  2018-07-25       Impact factor: 5.221

10.  Surface similarity-based molecular query-retrieval.

Authors:  Rahul Singh
Journal:  BMC Cell Biol       Date:  2007-07-10       Impact factor: 4.241
  10 in total

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