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)

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)

Optimal contact definition for reconstruction of Contact Maps. - Jose M. Duarte; Rajagopal Sathyapriya; Henning Stehr; Ioannis Filippis; Michael Lappe (BMC Bioinform., 2010)

CMView: Interactive contact map visualization and analysis. - Corinna Vehlow; Henning Stehr; Matthias Winkelmann; Jose M. Duarte; Lars Petzold; Juliane Dinse; Michael Lappe (Bioinform., 2011)

Protein interface classification by evolutionary analysis. - Jose M. Duarte; Adam Srebniak; Martin A. Schärer; Guido Capitani (BMC Bioinform., 2012)

Web-based molecular graphics for large complexes. - Alexander S. Rose; Anthony R. Bradley; Yana Valasatava; Jose M. Duarte; Andreas Prlic; Peter W. Rose (Web3D, 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)

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; et al. (Nucleic Acids Res., 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)

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)

Automated evaluation of quaternary structures from protein crystals. - Spencer Bliven; Aleix Lafita; Althea Parker; Guido Capitani; Jose M. Duarte (PLoS Comput. Biol., 2018)

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 022; Luigi Di Costanzo; Cole H. Christie; Kenneth Dalenberg; Jose M. Duarte; Shuchismita Dutta; Zukang Feng; Sutapa Ghosh; et al. (Nucleic Acids Res., 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; et al. (PLoS Comput. Biol., 2019)

Real time structural search of the Protein Data Bank. - Dmytro Guzenko; Stephen K. Burley; Jose M. Duarte (PLoS Comput. Biol., 2020)

RCSB Protein Data Bank 1D tools and services. - Joan Segura; Yana Rose; John D. Westbrook; Stephen K. Burley; Jose M. Duarte (Bioinform., 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 022; Gregg V. Crichlow; Cole H. Christie; Kenneth Dalenberg; Luigi Di Costanzo; Jose M. Duarte; Shuchismita Dutta; Zukang Feng; et al. (Nucleic Acids Res., 2021)

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)

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 (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 022; Paul A. Craig; Gregg V. Crichlow; Kenneth Dalenberg; Jose M. Duarte; Shuchismita Dutta; Maryam Fayazi; et al. (Nucleic Acids Res., 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., 2023)