Alexander S. Rose

Publication Activity (10 Years)

Years Active: 2009-2023
Publications (10 Years): 20

Top Topics

Convolutional Neural Networks

Molecular Structures

Top Venues

Nucleic Acids Res.

PLoS Comput. Biol.

Publications

Aliaksei Chareshneu, Adam Midlik, Crina-Maria Ionescu, Alexander S. Rose, Vladimír Horský, Alessio Cantara, Radka Svobodová Vareková, Karel Berka, David Sehnal
Mol* Volumes and Segmentations: visualization and interpretation of cell imaging data alongside macromolecular structure data and biological annotations. Nucleic Acids Res. 51 (W1) (2023)
Michelle Kampfrath, René Staritzbichler, Guillermo Pérez Hernández, Alexander S. Rose, Johanna K. S. Tiemann, Gerik Scheuermann, Daniel Wiegreffe, Peter W. Hildebrand
MDsrv: visual sharing and analysis of molecular dynamics simulations. Nucleic Acids Res. 50 (W1) (2022)
Michelle Kampfrath, René Staritzbichler, Guillermo Pérez Hernández, Alexander S. Rose, Johanna K. S. Tiemann, Gerik Scheuermann, Daniel Wiegreffe, Peter W. Hildebrand
MDsrv - visual sharing and analysis of molecular dynamics simulations. CoRR (2022)
Stephen K. Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich, Li Chen, Gregg V. Crichlow, Cole H. Christie, Kenneth Dalenberg, Luigi Di Costanzo, Jose M. Duarte, Shuchismita Dutta, Zukang Feng, Sai Ganesan, David S. Goodsell, Sutapa Ghosh, Rachel Kramer Green, Vladimir Guranovic, Dmytro Guzenko, Brian P. Hudson, Catherine L. Lawson, Yuhe Liang, Robert Lowe, Harry Namkoong, Ezra Peisach, Irina Persikova, Christopher Randle, Alexander S. Rose, Yana Rose, Andrej Sali, Joan Segura, Monica Sekharan, Chenghua Shao, Yi-Ping Tao, Maria Voigt, John D. Westbrook, Jasmine Young, Christine Zardecki, Marina Zhuravleva
RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. Nucleic Acids Res. 49 (Database-Issue) (2021)
Karsten Schatz, Juan José Franco-Moreno, Marco Schäfer, Alexander S. Rose, Valerio Ferrario, Jürgen Pleiss, Pere-Pau Vázquez, Thomas Ertl, Michael Krone
Visual Analysis of Large-Scale Protein-Ligand Interaction Data. Comput. Graph. Forum 40 (6) (2021)
David Sehnal, Sebastian Bittrich, Mandar S. Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K. Burley, Jaroslav Koca, Alexander S. Rose
Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. Nucleic Acids Res. 49 (Webserver-Issue) (2021)
Sebastian Bittrich, Stephen K. Burley, Alexander S. Rose
Real-time structural motif searching in proteins using an inverted index strategy. PLoS Comput. Biol. 16 (12) (2020)
David Sehnal, Sebastian Bittrich, Sameer Velankar, Jaroslav Koca, Radka Svobodová Vareková, Stephen K. Burley, Alexander S. Rose
BinaryCIF and CIFTools - Lightweight, efficient and extensible macromolecular data management. PLoS Comput. Biol. 16 (10) (2020)
Stephen K. Burley, Helen M. Berman, Charmi Bhikadiya, Chunxiao Bi, Li Chen, Luigi Di Costanzo, Cole H. Christie, Kenneth Dalenberg, Jose M. Duarte, Shuchismita Dutta, Zukang Feng, Sutapa Ghosh, David S. Goodsell, Rachel Kramer Green, Vladimir Guranovic, Dmytro Guzenko, Brian P. Hudson, Tara Kalro, Yuhe Liang, Robert Lowe, Harry Namkoong, Ezra Peisach, Irina Periskova, Andreas Prlic, Christopher Randle, Alexander S. Rose, Peter W. Rose, Raul Sala, Monica Sekharan, Chenghua Shao, Lihua Tan, Yi-Ping Tao, Yana Valasatava, Maria Voigt, John D. Westbrook, Jesse Woo, Huanwang Yang, Jasmine Young, Marina Zhuravleva, Christine Zardecki
RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy. Nucleic Acids Res. 47 (Database-Issue) (2019)
Hai Nguyen, David A. Case, Alexander S. Rose
NGLview-interactive molecular graphics for Jupyter notebooks. Bioinform. 34 (7) (2018)
Johanna K. S. Tiemann, Alexander S. Rose, Jochen Ismer, Mitra D. Darvish, Tarek Hilal, Christian M. T. Spahn, Peter W. Hildebrand
FragFit: a web-application for interactive modeling of protein segments into cryo-EM density maps. Nucleic Acids Res. 46 (Webserver-Issue) (2018)
David Sehnal, Alexander S. Rose, Jaroslav Koca, Stephen K. Burley, Sameer Velankar
Mol*: Towards a Common Library and Tools for Web Molecular Graphics. MolVa@EuroVis (2018)
Alexander S. Rose, Anthony R. Bradley, Yana Valasatava, Jose M. Duarte, Andreas Prlic, Peter W. Rose
NGL viewer: web-based molecular graphics for large complexes. Bioinform. 34 (21) (2018)
Peter W. Rose, Andreas Prlic, Ali Altunkaya, Chunxiao Bi, Anthony R. Bradley, Cole H. Christie, Luigi Di Costanzo, Jose M. Duarte, Shuchismita Dutta, Zukang Feng, Rachel Kramer Green, David S. Goodsell, Brian P. Hudson, Tara Kalro, Robert Lowe, Ezra Peisach, Christopher Randle, Alexander S. Rose, Chenghua Shao, Yi-Ping Tao, Yana Valasatava, Maria Voigt, John D. Westbrook, Jesse Woo, Huanwang Yang, Jasmine Young, Christine Zardecki, Helen M. Berman, Stephen K. Burley
The RCSB protein data bank: integrative view of protein, gene and 3D structural information. Nucleic Acids Res. 45 (Database-Issue) (2017)
Naif Alharbi, Mohammad Alharbi, Xavier Martinez, Michael Krone, Alexander S. Rose, Marc Baaden, Robert S. Laramee, Matthieu Chavent
Molecular Visualization of Computational Biology Data: A Survey of Surveys. EuroVis (Short Papers) (2017)
Jochen Ismer, Alexander S. Rose, Johanna K. S. Tiemann, Peter W. Hildebrand
A fragment based method for modeling of protein segments into cryo-EM density maps. BMC Bioinform. 18 (1) (2017)
José Jiménez, Stefan Doerr, Gerard Martínez-Rosell, Alexander S. Rose, Gianni De Fabritiis
DeepSite: protein-binding site predictor using 3D-convolutional neural networks. Bioinform. 33 (19) (2017)
Anthony R. Bradley, Alexander S. Rose, Antonín Pavelka, Yana Valasatava, Jose M. Duarte, Andreas Prlic, Peter W. Rose
MMTF - An efficient file format for the transmission, visualization, and analysis of macromolecular structures. PLoS Comput. Biol. 13 (6) (2017)
Jochen Ismer, Alexander S. Rose, Johanna K. S. Tiemann, Andrean Goede, Robert Preissner, Peter W. Hildebrand
SL2: an interactive webtool for modeling of missing segments in proteins. Nucleic Acids Res. 44 (Webserver-Issue) (2016)
Alexander S. Rose, Anthony R. Bradley, Yana Valasatava, Jose M. Duarte, Andreas Prlic, Peter W. Rose
Web-based molecular graphics for large complexes. Web3D (2016)
Alexander S. Rose, Peter W. Hildebrand
NGL Viewer: a web application for molecular visualization. Nucleic Acids Res. 43 (Webserver-Issue) (2015)
Alexander S. Rose, Dominic Theune, Andrean Goede, Peter Werner Hildebrand
MP: PD - a data base of internal packing densities, internal packing defects and internal waters of helical membrane proteins. Nucleic Acids Res. 42 (Database-Issue) (2014)
Jochen Ismer, Alexander S. Rose, Johanna K. S. Tiemann, Andrean Goede, Kristian Rother, Peter Werner Hildebrand
Voronoia4RNA - a database of atomic packing densities of RNA structures and their complexes. Nucleic Acids Res. 41 (Database-Issue) (2013)
Alexander S. Rose, Andrean Goede, Peter Werner Hildebrand
MPlot - a server to analyze and visualize tertiary structure contacts and geometrical features of helical membrane proteins. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)
Alexander S. Rose, Stephan Lorenzen, Andrean Goede, Björn A. Grüning, Peter Werner Hildebrand
RHYTHM - a server to predict the orientation of transmembrane helices in channels and membrane-coils. Nucleic Acids Res. 37 (Web-Server-Issue) (2009)