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Literature DB >> 23337870

Trendspotting in the Protein Data Bank.

Helen M Berman¹, Buvaneswari Coimbatore Narayanan, Luigi Di Costanzo, Shuchismita Dutta, Sutapa Ghosh, Brian P Hudson, Catherine L Lawson, Ezra Peisach, Andreas Prlić, Peter W Rose, Chenghua Shao, Huanwang Yang, Jasmine Young, Christine Zardecki.

Abstract

The Protein Data Bank (PDB) was established in 1971 as a repository for the three dimensional structures of biological macromolecules. Since then, more than 85000 biological macromolecule structures have been determined and made available in the PDB archive. Through analysis of the corpus of data, it is possible to identify trends that can be used to inform us abou the future of structural biology and to plan the best ways to improve the management of the ever-growing amount of PDB data.

Entities: Chemical Disease Gene Species

Mesh：

Substances：
Nucleic Acids
Proteins

Year: 2013 PMID： 23337870 PMCID： PMC4068610 DOI： 10.1016/j.febslet.2012.12.029

Source DB: PubMed Journal: FEBS Lett ISSN： 0014-5793 Impact factor: 4.124

53 in total

1. The Protein Data Bank.

Authors: H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal: Nucleic Acids Res Date: 2000-01-01 Impact factor: 16.971

2. Announcing the worldwide Protein Data Bank.

Authors: Helen Berman; Kim Henrick; Haruki Nakamura
Journal: Nat Struct Biol Date: 2003-12

3. Structure of a 16-nm cage designed by using protein oligomers.

Authors: Yen-Ting Lai; Duilio Cascio; Todd O Yeates
Journal: Science Date: 2012-06-01 Impact factor: 47.728

4. Crystal structure of a hepatitis delta virus ribozyme.

Authors: A R Ferré-D'Amaré; K Zhou; J A Doudna
Journal: Nature Date: 1998-10-08 Impact factor: 49.962

5. Chemical engineering of Mycobacterium tuberculosis dodecin hybrids.

Authors: Xenia Vinzenz; Wolfgang Grosse; Uwe Linne; Britta Meissner; Lars-Oliver Essen
Journal: Chem Commun (Camb) Date: 2011-09-06 Impact factor: 6.222

6. Molecular structure of a left-handed double helical DNA fragment at atomic resolution.

Authors: A H Wang; G J Quigley; F J Kolpak; J L Crawford; J H van Boom; G van der Marel; A Rich
Journal: Nature Date: 1979-12-13 Impact factor: 49.962

7. Atomic co-ordinates for yeast phenylalanine tRNA.

Authors: J E Ladner; A Jack; J D Robertus; R S Brown; D Rhodes; B F Clark; A Klug
Journal: Nucleic Acids Res Date: 1975-09 Impact factor: 16.971

8. Structure of human chitotriosidase. Implications for specific inhibitor design and function of mammalian chitinase-like lectins.

Authors: Fabrizia Fusetti; Holger von Moeller; Douglas Houston; Henriette J Rozeboom; Bauke W Dijkstra; Rolf G Boot; Johannes M F G Aerts; Daan M F van Aalten
Journal: J Biol Chem Date: 2002-04-17 Impact factor: 5.157

9. The Protein Structure Initiative: achievements and visions for the future.

Authors: Gaetano T Montelione
Journal: F1000 Biol Rep Date: 2012-04-02

10. Outcome of the first electron microscopy validation task force meeting.

Authors: Richard Henderson; Andrej Sali; Matthew L Baker; Bridget Carragher; Batsal Devkota; Kenneth H Downing; Edward H Egelman; Zukang Feng; Joachim Frank; Nikolaus Grigorieff; Wen Jiang; Steven J Ludtke; Ohad Medalia; Pawel A Penczek; Peter B Rosenthal; Michael G Rossmann; Michael F Schmid; Gunnar F Schröder; Alasdair C Steven; David L Stokes; John D Westbrook; Willy Wriggers; Huanwang Yang; Jasmine Young; Helen M Berman; Wah Chiu; Gerard J Kleywegt; Catherine L Lawson
Journal: Structure Date: 2012-02-08 Impact factor: 5.006

37 in total

Review 10. Coverage of protein domain families with structural protein-protein interactions: current progress and future trends.

Authors: Alexander Goncearenco; Benjamin A Shoemaker; Dachuan Zhang; Alexey Sarychev; Anna R Panchenko
Journal: Prog Biophys Mol Biol Date: 2014-06-13 Impact factor: 3.667

Trendspotting in the Protein Data Bank.

1. The Protein Data Bank.

2. Announcing the worldwide Protein Data Bank.

3. Structure of a 16-nm cage designed by using protein oligomers.

4. Crystal structure of a hepatitis delta virus ribozyme.

5. Chemical engineering of Mycobacterium tuberculosis dodecin hybrids.

6. Molecular structure of a left-handed double helical DNA fragment at atomic resolution.

7. Atomic co-ordinates for yeast phenylalanine tRNA.

8. Structure of human chitotriosidase. Implications for specific inhibitor design and function of mammalian chitinase-like lectins.

9. The Protein Structure Initiative: achievements and visions for the future.

10. Outcome of the first electron microscopy validation task force meeting.

Review 1. 50 years of allosteric interactions: the twists and turns of the models.

2. Quantifying sequence and structural features of protein-RNA interactions.

Review 3. X-ray crystallography over the past decade for novel drug discovery - where are we heading next?

4. Synchrotron-based macromolecular crystallography module for an undergraduate biochemistry laboratory course.

5. Automatic recognition of ligands in electron density by machine learning.

6. Redundancy-weighting for better inference of protein structural features.

7. A close-up view of codon selection in eukaryotic initiation.

8. Iterative Molecular Dynamics-Rosetta Membrane Protein Structure Refinement Guided by Cryo-EM Densities.

9. Improving inverse docking target identification with Z-score selection.

Review 10. Coverage of protein domain families with structural protein-protein interactions: current progress and future trends.