Literature DB >> 15766539

Large macromolecular complexes in the Protein Data Bank: a status report.

Shuchismita Dutta1, Helen M Berman.   

Abstract

The growing number of large macromolecular complexes in the Protein Data Bank (PDB) has warranted a closer look at these structures. An overview of the types of molecules that form these large complexes is presented here. Some of the challenges at the PDB in representing, archiving, visualizing, and analyzing these structures are discussed along with possible means to overcome them.

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Year:  2005        PMID: 15766539     DOI: 10.1016/j.str.2005.01.008

Source DB:  PubMed          Journal:  Structure        ISSN: 0969-2126            Impact factor:   5.006


  21 in total

1.  Macromolecular docking restrained by a small angle X-ray scattering profile.

Authors:  Dina Schneidman-Duhovny; Michal Hammel; Andrej Sali
Journal:  J Struct Biol       Date:  2010-10-12       Impact factor: 2.867

2.  FR3D: finding local and composite recurrent structural motifs in RNA 3D structures.

Authors:  Michael Sarver; Craig L Zirbel; Jesse Stombaugh; Ali Mokdad; Neocles B Leontis
Journal:  J Math Biol       Date:  2007-08-11       Impact factor: 2.259

Review 3.  Visualization software for molecular assemblies.

Authors:  Thomas D Goddard; Thomas E Ferrin
Journal:  Curr Opin Struct Biol       Date:  2007-08-28       Impact factor: 6.809

Review 4.  Data deposition and annotation at the worldwide protein data bank.

Authors:  Shuchismita Dutta; Kyle Burkhardt; Jasmine Young; Ganesh J Swaminathan; Takanori Matsuura; Kim Henrick; Haruki Nakamura; Helen M Berman
Journal:  Mol Biotechnol       Date:  2008-12-10       Impact factor: 2.695

5.  BCL::EM-Fit: rigid body fitting of atomic structures into density maps using geometric hashing and real space refinement.

Authors:  Nils Woetzel; Steffen Lindert; Phoebe L Stewart; Jens Meiler
Journal:  J Struct Biol       Date:  2011-05-04       Impact factor: 2.867

6.  CASP10-BCL::Fold efficiently samples topologies of large proteins.

Authors:  Sten Heinze; Daniel K Putnam; Axel W Fischer; Tim Kohlmann; Brian E Weiner; Jens Meiler
Journal:  Proteins       Date:  2015-03

7.  A multiscale model for virus capsid dynamics.

Authors:  Changjun Chen; Rishu Saxena; Guo-Wei Wei
Journal:  Int J Biomed Imaging       Date:  2010-03-09

8.  Structural Perspectives on the Evolutionary Expansion of Unique Protein-Protein Binding Sites.

Authors:  Alexander Goncearenco; Alexey K Shaytan; Benjamin A Shoemaker; Anna R Panchenko
Journal:  Biophys J       Date:  2015-07-23       Impact factor: 4.033

9.  Representation of viruses in the remediated PDB archive.

Authors:  Catherine L Lawson; Shuchismita Dutta; John D Westbrook; Kim Henrick; Helen M Berman
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2008-07-17

10.  The interwinding nature of protein-protein interfaces and its implication for protein complex formation.

Authors:  Kei Yura; Steven Hayward
Journal:  Bioinformatics       Date:  2009-09-29       Impact factor: 6.937

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