Literature DB >> 8440755

New method for rapid characterization of molecular shapes: applications in drug design.

R Nilakantan1, N Bauman, R Venkataraghavan.   

Abstract

We present a method for the rapid quantitative shape match between two molecules or a molecule and a template, using atom triplets as descriptors. This technique can be used either as a rapid screen preceding the computationally expensive shape-based docking method developed by Kuntz and co-workers or as a stand-alone method to rank compounds in a large database for their fit to a shape template. The merits and limitations of this method are discussed in detail with examples.

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Year:  1993        PMID: 8440755     DOI: 10.1021/ci00011a012

Source DB:  PubMed          Journal:  J Chem Inf Comput Sci        ISSN: 0095-2338


  11 in total

1.  Measuring CAMD technique performance: a virtual screening case study in the design of validation experiments.

Authors:  Andrew C Good; Mark A Hermsmeier; S A Hindle
Journal:  J Comput Aided Mol Des       Date:  2004 Jul-Sep       Impact factor: 3.686

Review 2.  Single enzyme nanoparticle, an effective tool for enzyme replacement therapy.

Authors:  Dong Hyun Kim; Han Sol Lee; Tae-Wan Kwon; Young-Min Han; Nae-Won Kang; Mee Yeon Lee; Dae-Duk Kim; Myeong Gyu Kim; Jae-Young Lee
Journal:  Arch Pharm Res       Date:  2020-01-27       Impact factor: 4.946

3.  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

4.  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

5.  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

6.  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

7.  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 8.  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

9.  Three dimensional shape comparison of flexible proteins using the local-diameter descriptor.

Authors:  Yi Fang; Yu-Shen Liu; Karthik Ramani
Journal:  BMC Struct Biol       Date:  2009-05-12

10.  Layers: A molecular surface peeling algorithm and its applications to analyze protein structures.

Authors:  Naga Bhushana Rao Karampudi; Ranjit Prasad Bahadur
Journal:  Sci Rep       Date:  2015-11-10       Impact factor: 4.379

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