Jose M. Duarte

According to our database, Jose M. Duarte authored at least 20 papers between 2009 and 2023.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2023

RCSB Protein Data Bank: visualizing groups of experimentally determined PDB structures alongside computed structure models of proteins.

Joan Segura, Yana Rose, Chunxiao Bi, Jose M. Duarte, Stephen K. Burley, Sebastian Bittrich

Frontiers Bioinform., May, 2023

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.

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

Nucleic Acids Res., January, 2023

2022

RCSB Protein Data Bank 1D3D module: displaying positional features on macromolecular assemblies.

Joan Segura, Yana Rose, Sebastian Bittrich, Stephen K. Burley, Jose M. Duarte

Bioinform., 2022

RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB.

Sebastian Bittrich, Yana Rose, Joan Segura, Robert Lowe, John D. Westbrook, Jose M. Duarte, Stephen K. Burley

Bioinform., 2022

2021

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.

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

Nucleic Acids Res., 2021

RCSB Protein Data Bank 1D tools and services.

Joan Segura, Yana Rose, John D. Westbrook, Stephen K. Burley, Jose M. Duarte

Bioinform., 2021

2020

Real time structural search of the Protein Data Bank.

Dmytro Guzenko, Stephen K. Burley, Jose M. Duarte

PLoS Comput. Biol., 2020

2019

BioJava 5: A community driven open-source bioinformatics library.

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

PLoS Comput. Biol., 2019

RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy.

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

Nucleic Acids Res., 2019

2018

Automated evaluation of quaternary structures from protein crystals.

Spencer Bliven, Aleix Lafita, Althea Parker, Guido Capitani, Jose M. Duarte

PLoS Comput. Biol., 2018

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

Alexander S. Rose, Anthony R. Bradley, Yana Valasatava, Jose M. Duarte, Andreas Prlic, Peter W. Rose

Bioinform., 2018

2017

MMTF - An efficient file format for the transmission, visualization, and analysis of macromolecular structures.

Anthony R. Bradley, Alexander S. Rose, Antonín Pavelka, Yana Valasatava, Jose M. Duarte, Andreas Prlic, Peter W. Rose

PLoS Comput. Biol., 2017

The RCSB protein data bank: integrative view of protein, gene and 3D structural information.

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

Nucleic Acids Res., 2017

2016

Understanding the fabric of protein crystals: computational classification of biological interfaces and crystal contacts.

Guido Capitani, Jose M. Duarte, Kumaran Baskaran, Spencer Bliven, Joseph C. Somody

Bioinform., 2016

Web-based molecular graphics for large complexes.

Alexander S. Rose, Anthony R. Bradley, Yana Valasatava, Jose M. Duarte, Andreas Prlic, Peter W. Rose

Proceedings of the 21st International Conference on Web3D Technology, 2016

2012

Protein interface classification by evolutionary analysis.

Jose M. Duarte, Adam Srebniak, Martin A. Schärer, Guido Capitani

BMC Bioinform., 2012

2011

CMView: Interactive contact map visualization and analysis.

Corinna Vehlow, Henning Stehr, Matthias Winkelmann, Jose M. Duarte, Lars Petzold, Juliane Dinse, Michael Lappe

Bioinform., 2011

2010

Optimal contact definition for reconstruction of Contact Maps.

Jose M. Duarte, Rajagopal Sathyapriya, Henning Stehr, Ioannis Filippis, Michael Lappe

BMC Bioinform., 2010

PDBWiki: added value through community annotation of the Protein Data Bank.

Henning Stehr, Jose M. Duarte, Michael Lappe, Jong Bhak, Dan M. Bolser

Database J. Biol. Databases Curation, 2010

2009

Defining an Essence of Structure Determining Residue Contacts in Proteins.

Rajagopal Sathyapriya, Jose M. Duarte, Henning Stehr, Ioannis Filippis, Michael Lappe

PLoS Comput. Biol., 2009