Literature DB >> 25633501

Aquaria: simplifying discovery and insight from protein structures.

Seán I O'Donoghue1, Kenneth S Sabir2, Maria Kalemanov3, Christian Stolte4, Benjamin Wellmann3, Vivian Ho5, Manfred Roos3, Nelson Perdigão6, Fabian A Buske7, Julian Heinrich4, Burkhard Rost3, Andrea Schafferhans3.   

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Year:  2015        PMID: 25633501     DOI: 10.1038/nmeth.3258

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   28.547


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  7 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.  AstexViewer: a visualisation aid for structure-based drug design.

Authors:  Michael J Hartshorn
Journal:  J Comput Aided Mol Des       Date:  2002-12       Impact factor: 3.686

3.  UCSF Chimera--a visualization system for exploratory research and analysis.

Authors:  Eric F Pettersen; Thomas D Goddard; Conrad C Huang; Gregory S Couch; Daniel M Greenblatt; Elaine C Meng; Thomas E Ferrin
Journal:  J Comput Chem       Date:  2004-10       Impact factor: 3.376

4.  The SRS 3D module: integrating structures, sequences and features.

Authors:  Seán I O'Donoghue; Joachim E W Meyer; Andrea Schafferhans; Karsten Fries
Journal:  Bioinformatics       Date:  2004-04-15       Impact factor: 6.937

5.  InterPro in 2011: new developments in the family and domain prediction database.

Authors:  Sarah Hunter; Philip Jones; Alex Mitchell; Rolf Apweiler; Teresa K Attwood; Alex Bateman; Thomas Bernard; David Binns; Peer Bork; Sarah Burge; Edouard de Castro; Penny Coggill; Matthew Corbett; Ujjwal Das; Louise Daugherty; Lauranne Duquenne; Robert D Finn; Matthew Fraser; Julian Gough; Daniel Haft; Nicolas Hulo; Daniel Kahn; Elizabeth Kelly; Ivica Letunic; David Lonsdale; Rodrigo Lopez; Martin Madera; John Maslen; Craig McAnulla; Jennifer McDowall; Conor McMenamin; Huaiyu Mi; Prudence Mutowo-Muellenet; Nicola Mulder; Darren Natale; Christine Orengo; Sebastien Pesseat; Marco Punta; Antony F Quinn; Catherine Rivoire; Amaia Sangrador-Vegas; Jeremy D Selengut; Christian J A Sigrist; Maxim Scheremetjew; John Tate; Manjulapramila Thimmajanarthanan; Paul D Thomas; Cathy H Wu; Corin Yeats; Siew-Yit Yong
Journal:  Nucleic Acids Res       Date:  2011-11-16       Impact factor: 16.971

6.  Activities at the Universal Protein Resource (UniProt).

Authors: 
Journal:  Nucleic Acids Res       Date:  2013-11-18       Impact factor: 16.971

Review 7.  Visualization of macromolecular structures.

Authors:  Seán I O'Donoghue; David S Goodsell; Achilleas S Frangakis; Fabrice Jossinet; Roman A Laskowski; Michael Nilges; Helen R Saibil; Andrea Schafferhans; Rebecca C Wade; Eric Westhof; Arthur J Olson
Journal:  Nat Methods       Date:  2010-03-01       Impact factor: 28.547

  7 in total
  20 in total

1.  Unexpected features of the dark proteome.

Authors:  Nelson Perdigão; Julian Heinrich; Christian Stolte; Kenneth S Sabir; Michael J Buckley; Bruce Tabor; Beth Signal; Brian S Gloss; Christopher J Hammang; Burkhard Rost; Andrea Schafferhans; Seán I O'Donoghue
Journal:  Proc Natl Acad Sci U S A       Date:  2015-11-17       Impact factor: 11.205

2.  iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures.

Authors:  Jiyao Wang; Philippe Youkharibache; Dachuan Zhang; Christopher J Lanczycki; Renata C Geer; Thomas Madej; Lon Phan; Minghong Ward; Shennan Lu; Gabriele H Marchler; Yanli Wang; Stephen H Bryant; Lewis Y Geer; Aron Marchler-Bauer
Journal:  Bioinformatics       Date:  2020-01-01       Impact factor: 6.937

Review 3.  To be disordered or not to be disordered: is that still a question for proteins in the cell?

Authors:  Kris Pauwels; Pierre Lebrun; Peter Tompa
Journal:  Cell Mol Life Sci       Date:  2017-06-13       Impact factor: 9.261

4.  TWIST1 Homodimers and Heterodimers Orchestrate Lineage-Specific Differentiation.

Authors:  Xiaochen Fan; Ashley J Waardenberg; Madeleine Demuth; Pierre Osteil; Jane Q J Sun; David A F Loebel; Mark Graham; Patrick P L Tam; Nicolas Fossat
Journal:  Mol Cell Biol       Date:  2020-05-14       Impact factor: 4.272

5.  ProteoVision: web server for advanced visualization of ribosomal proteins.

Authors:  Petar I Penev; Holly M McCann; Caeden D Meade; Claudia Alvarez-Carreño; Aparna Maddala; Chad R Bernier; Vasanta L Chivukula; Maria Ahmad; Burak Gulen; Aakash Sharma; Loren Dean Williams; Anton S Petrov
Journal:  Nucleic Acids Res       Date:  2021-07-02       Impact factor: 16.971

6.  PyMine: a PyMOL plugin to integrate and visualize data for drug discovery.

Authors:  Rajan Chaudhari; Zhijun Li
Journal:  BMC Res Notes       Date:  2015-10-01

7.  SANSparallel: interactive homology search against Uniprot.

Authors:  Panu Somervuo; Liisa Holm
Journal:  Nucleic Acids Res       Date:  2015-04-08       Impact factor: 16.971

8.  Targeting Thioredoxin-1 by dimethyl fumarate induces ripoptosome-mediated cell death.

Authors:  Anne Schroeder; Uwe Warnken; Daniel Röth; Karel D Klika; Diana Vobis; Andrea Barnert; Fatmire Bujupi; Tina Oberacker; Martina Schnölzer; Jan P Nicolay; Peter H Krammer; Karsten Gülow
Journal:  Sci Rep       Date:  2017-02-24       Impact factor: 4.379

9.  PredictProtein - Predicting Protein Structure and Function for 29 Years.

Authors:  Michael Bernhofer; Christian Dallago; Tim Karl; Venkata Satagopam; Michael Heinzinger; Maria Littmann; Tobias Olenyi; Jiajun Qiu; Konstantin Schütze; Guy Yachdav; Haim Ashkenazy; Nir Ben-Tal; Yana Bromberg; Tatyana Goldberg; Laszlo Kajan; Sean O'Donoghue; Chris Sander; Andrea Schafferhans; Avner Schlessinger; Gerrit Vriend; Milot Mirdita; Piotr Gawron; Wei Gu; Yohan Jarosz; Christophe Trefois; Martin Steinegger; Reinhard Schneider; Burkhard Rost
Journal:  Nucleic Acids Res       Date:  2021-07-02       Impact factor: 16.971

10.  Integrated visual analysis of protein structures, sequences, and feature data.

Authors:  Christian Stolte; Kenneth S Sabir; Julian Heinrich; Christopher J Hammang; Andrea Schafferhans; Seán I O'Donoghue
Journal:  BMC Bioinformatics       Date:  2015-08-13       Impact factor: 3.169

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