Literature DB >> 29190272

LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data.

David Sehnal1,2,3, Mandar Deshpande3, Radka Svobodová Vařeková1,2, Saqib Mir3, Karel Berka4, Adam Midlik1,2, Lukáš Pravda1,2, Sameer Velankar3, Jaroslav Koča1,2.   

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Year:  2017        PMID： 29190272     DOI： 10.1038/nmeth.4499

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


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  6 in total

1.  New electron microscopy database and deposition system.

Authors:  Mohamed Tagari; Richard Newman; Monica Chagoyen; Jose Maria Carazo; Kim Henrick
Journal:  Trends Biochem Sci       Date:  2002-11       Impact factor: 13.807

2.  Announcing the worldwide Protein Data Bank.

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

3.  PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank.

Authors:  David Sehnal; Lukáš Pravda; Radka Svobodová Vařeková; Crina-Maria Ionescu; Jaroslav Koča
Journal:  Nucleic Acids Res       Date:  2015-05-26       Impact factor: 16.971

4.  PDBe: improved accessibility of macromolecular structure data from PDB and EMDB.

Authors:  Sameer Velankar; Glen van Ginkel; Younes Alhroub; Gary M Battle; John M Berrisford; Matthew J Conroy; Jose M Dana; Swanand P Gore; Aleksandras Gutmanas; Pauline Haslam; Pieter M S Hendrickx; Ingvar Lagerstedt; Saqib Mir; Manuel A Fernandez Montecelo; Abhik Mukhopadhyay; Thomas J Oldfield; Ardan Patwardhan; Eduardo Sanz-García; Sanchayita Sen; Robert A Slowley; Michael E Wainwright; Mandar S Deshpande; Andrii Iudin; Gaurav Sahni; Jose Salavert Torres; Miriam Hirshberg; Lora Mak; Nurul Nadzirin; David R Armstrong; Alice R Clark; Oliver S Smart; Paul K Korir; Gerard J Kleywegt
Journal:  Nucleic Acids Res       Date:  2015-10-17       Impact factor: 16.971

5.  Towards an efficient compression of 3D coordinates of macromolecular structures.

Authors:  Yana Valasatava; Anthony R Bradley; Alexander S Rose; Jose M Duarte; Andreas Prlić; Peter W Rose
Journal:  PLoS One       Date:  2017-03-31       Impact factor: 3.240

Review 6.  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
  6 in total
  52 in total

1.  NGL viewer: web-based molecular graphics for large complexes.

Authors:  Alexander S Rose; Anthony R Bradley; Yana Valasatava; Jose M Duarte; Andreas Prlic; Peter W Rose
Journal:  Bioinformatics       Date:  2018-11-01       Impact factor: 6.937

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

3.  Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB).

Authors:  Paul D Adams; Pavel V Afonine; Kumaran Baskaran; Helen M Berman; John Berrisford; Gerard Bricogne; David G Brown; Stephen K Burley; Minyu Chen; Zukang Feng; Claus Flensburg; Aleksandras Gutmanas; Jeffrey C Hoch; Yasuyo Ikegawa; Yumiko Kengaku; Eugene Krissinel; Genji Kurisu; Yuhe Liang; Dorothee Liebschner; Lora Mak; John L Markley; Nigel W Moriarty; Garib N Murshudov; Martin Noble; Ezra Peisach; Irina Persikova; Billy K Poon; Oleg V Sobolev; Eldon L Ulrich; Sameer Velankar; Clemens Vonrhein; John Westbrook; Marcin Wojdyr; Masashi Yokochi; Jasmine Y Young
Journal:  Acta Crystallogr D Struct Biol       Date:  2019-04-08       Impact factor: 7.652

4.  The Protein Data Bank Archive.

Authors:  Sameer Velankar; Stephen K Burley; Genji Kurisu; Jeffrey C Hoch; John L Markley
Journal:  Methods Mol Biol       Date:  2021

5.  GlyMDB: Glycan Microarray Database and analysis toolset.

Authors:  Yiwei Cao; Sang-Jun Park; Akul Y Mehta; Richard D Cummings; Wonpil Im
Journal:  Bioinformatics       Date:  2020-04-15       Impact factor: 6.937

6.  An Interactive View of Glycosylation.

Authors:  Julien Mariethoz; Davide Alocci; Niclas G Karlsson; Nicolle H Packer; Frédérique Lisacek
Journal:  Methods Mol Biol       Date:  2022

Review 7.  Perspectives on Structural Molecular Biology Visualization: From Past to Present.

Authors:  Arthur J Olson
Journal:  J Mol Biol       Date:  2018-07-23       Impact factor: 5.469

8.  MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update).

Authors:  Lukáš Pravda; David Sehnal; Dominik Toušek; Veronika Navrátilová; Václav Bazgier; Karel Berka; Radka Svobodová Vareková; Jaroslav Koca; Michal Otyepka
Journal:  Nucleic Acids Res       Date:  2018-07-02       Impact factor: 16.971

9.  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

10.  Proteome-wide prediction of bacterial carbohydrate-binding proteins as a tool for understanding commensal and pathogen colonisation of the vaginal microbiome.

Authors:  François Bonnardel; Stuart M Haslam; Anne Dell; Ten Feizi; Yan Liu; Virginia Tajadura-Ortega; Yukie Akune; Lynne Sykes; Phillip R Bennett; David A MacIntyre; Frédérique Lisacek; Anne Imberty
Journal:  NPJ Biofilms Microbiomes       Date:  2021-06-15       Impact factor: 7.290
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