Jose M. Duarte

22 papers Journal 21Unranked 1
YearRankTypeTitle / Venue / Authors
2026 J jnl
Multi-scale structural similarity embedding search across entire proteomes.
Bioinform.
Joan Segura, Rubén Sánchez García, Sebastian Bittrich, Yana Rose, Stephen K. Burley, Jose M. Duarte
2024 J jnl
RCSB protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments.
Bioinform.
Sebastian Bittrich, Joan Segura, Jose M. Duarte, Stephen K. Burley, Yana Rose
2023 J jnl
RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning.
Nucleic Acids Res.
Stephen K. Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich, Henry Chao, Li Chen, Paul A. Craig, Gregg V. Crichlow, Kenneth Dalenberg, Jose M. Duarte, Shuchismita Dutta, Maryam Fayazi, Zukang Feng, Justin W. Flatt, Sai Ganesan, Sutapa Ghosh, David S. Goodsell, Rachel Kramer Green, Vladimir Guranovic, Jeremy Henry, Brian P. Hudson, Igor Khokhriakov, Catherine L. Lawson, Yuhe Liang, Robert Lowe, Ezra Peisach, Irina Persikova, Dennis W. Piehl, Yana Rose, Andrej Sali, Joan Segura, Monica Sekharan, Chenghua Shao, Brinda Vallat, Maria Voigt, Ben M. Webb, John D. Westbrook, Shamara Whetstone, Jasmine Young, Arthur O. Zalevsky, Christine Zardecki
2023 J jnl
RCSB Protein Data Bank: visualizing groups of experimentally determined PDB structures alongside computed structure models of proteins.
Frontiers Bioinform.
Joan Segura, Yana Rose, Chunxiao Bi, Jose M. Duarte, Stephen K. Burley, Sebastian Bittrich
2022 J jnl
RCSB Protein Data Bank 1D3D module: displaying positional features on macromolecular assemblies.
Bioinform.
Joan Segura, Yana Rose, Sebastian Bittrich, Stephen K. Burley, Jose M. Duarte
2022 J jnl
RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB.
Bioinform.
Sebastian Bittrich, Yana Rose, Joan Segura, Robert Lowe, John D. Westbrook, Jose M. Duarte, Stephen K. Burley
2021 J jnl
RCSB Protein Data Bank 1D tools and services.
Bioinform.
Joan Segura, Yana Rose, John D. Westbrook, Stephen K. Burley, Jose M. Duarte
2021 J jnl
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.
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
2020 J jnl
Real time structural search of the Protein Data Bank.
PLoS Comput. Biol.
Dmytro Guzenko, Stephen K. Burley, Jose M. Duarte
2019 J jnl
BioJava 5: A community driven open-source bioinformatics library.
PLoS Comput. Biol.
Aleix Lafita, Spencer Bliven, Andreas Prlic, Dmytro Guzenko, Peter W. Rose, Anthony R. Bradley, Paolo Pavan, Douglas Myers-Turnbull, Yana Valasatava, Michael L. Heuer, Matt Larson, Stephen K. Burley, Jose M. Duarte
2019 J jnl
RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy.
Nucleic Acids Res.
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
2018 J jnl
Automated evaluation of quaternary structures from protein crystals.
PLoS Comput. Biol.
Spencer Bliven, Aleix Lafita, Althea Parker, Guido Capitani, Jose M. Duarte
2018 J jnl
NGL viewer: web-based molecular graphics for large complexes.
Bioinform.
Alexander S. Rose, Anthony R. Bradley, Yana Valasatava, Jose M. Duarte, Andreas Prlic, Peter W. Rose
2017 J jnl
MMTF - An efficient file format for the transmission, visualization, and analysis of macromolecular structures.
PLoS Comput. Biol.
Anthony R. Bradley, Alexander S. Rose, Antonín Pavelka, Yana Valasatava, Jose M. Duarte, Andreas Prlic, Peter W. Rose
2017 J jnl
The RCSB protein data bank: integrative view of protein, gene and 3D structural information.
Nucleic Acids Res.
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
2016 J jnl
Understanding the fabric of protein crystals: computational classification of biological interfaces and crystal contacts.
Bioinform.
Guido Capitani, Jose M. Duarte, Kumaran Baskaran, Spencer Bliven, Joseph C. Somody
2016 — conf
Web-based molecular graphics for large complexes.
Web3D
Alexander S. Rose, Anthony R. Bradley, Yana Valasatava, Jose M. Duarte, Andreas Prlic, Peter W. Rose
2012 J jnl
Protein interface classification by evolutionary analysis.
BMC Bioinform.
Jose M. Duarte, Adam Srebniak, Martin A. Schärer, Guido Capitani
2011 J jnl
CMView: Interactive contact map visualization and analysis.
Bioinform.
Corinna Vehlow, Henning Stehr, Matthias Winkelmann, Jose M. Duarte, Lars Petzold, Juliane Dinse, Michael Lappe
2010 J jnl
Optimal contact definition for reconstruction of Contact Maps.
BMC Bioinform.
Jose M. Duarte, Rajagopal Sathyapriya, Henning Stehr, Ioannis Filippis, Michael Lappe
2010 J jnl
PDBWiki: added value through community annotation of the Protein Data Bank.
Database J. Biol. Databases Curation
Henning Stehr, Jose M. Duarte, Michael Lappe, Jong Bhak, Dan M. Bolser
2009 J jnl
Defining an Essence of Structure Determining Residue Contacts in Proteins.
PLoS Comput. Biol.
Rajagopal Sathyapriya, Jose M. Duarte, Henning Stehr, Ioannis Filippis, Michael Lappe