Literature DB >> 9390238

On the definition and the construction of pockets in macromolecules.

H Edelsbrunner1, M Facello, J Liang.   

Abstract

The shape of a protein is important for its functions. This includes the location and size of identifiable regions in its complement space. We formally define pockets as regions in the complement with limited accessibility from the outside. Pockets can be efficiently constructed by an algorithm based on alpha complexes. The algorithm is implemented and applied to proteins with known three-dimensional conformations.

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Year:  1996        PMID: 9390238

Source DB:  PubMed          Journal:  Pac Symp Biocomput        ISSN: 2335-6928


  17 in total

1.  Classification of protein functional surfaces using structural characteristics.

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2.  Topology Based Selection and Curation of Level Sets.

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3.  Effective electrostatic charge of coagulation factor X in solution and on phospholipid membranes: implications for activation mechanisms and structure-function relationships of the Gla domain.

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Review 4.  Chapter 4. Predicting and characterizing protein functions through matching geometric and evolutionary patterns of binding surfaces.

Authors:  Jie Liang; Yan-Yuan Tseng; Joseph Dundas; T Andrew Binkowski; Andrzej Joachimiak; Zheng Ouyang; Larisa Adamian
Journal:  Adv Protein Chem Struct Biol       Date:  2009-02-26       Impact factor: 3.507

5.  Global and local molecular dynamics of a bacterial carboxylesterase provide insight into its catalytic mechanism.

Authors:  Xiaozhen Yu; Sara C Sigler; Delwar Hossain; Monika Wierdl; Steven R Gwaltney; Philip M Potter; Randy M Wadkins
Journal:  J Mol Model       Date:  2011-11-30       Impact factor: 1.810

6.  Ionizable side chains at catalytic active sites of enzymes.

Authors:  David Jimenez-Morales; Jie Liang; Bob Eisenberg
Journal:  Eur Biophys J       Date:  2012-04-07       Impact factor: 1.733

7.  Geometry of protein shape and its evolutionary pattern for function prediction and characterization.

Authors:  Jie Liang
Journal:  Conf Proc IEEE Eng Med Biol Soc       Date:  2009

8.  Structural model of rho1 GABAC receptor based on evolutionary analysis: Testing of predicted protein-protein interactions involved in receptor assembly and function.

Authors:  Larisa Adamian; Hélène A Gussin; Yan Yuan Tseng; Niraj J Muni; Feng Feng; Haohua Qian; David R Pepperberg; Jie Liang
Journal:  Protein Sci       Date:  2009-11       Impact factor: 6.725

9.  SplitPocket: identification of protein functional surfaces and characterization of their spatial patterns.

Authors:  Yan Yuan Tseng; Craig Dupree; Z Jeffrey Chen; Wen-Hsiung Li
Journal:  Nucleic Acids Res       Date:  2009-04-30       Impact factor: 16.971

10.  fPOP: footprinting functional pockets of proteins by comparative spatial patterns.

Authors:  Yan Yuan Tseng; Z Jeffrey Chen; Wen-Hsiung Li
Journal:  Nucleic Acids Res       Date:  2009-10-30       Impact factor: 16.971

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