Jose M Duarte

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 20

Top Topics

Protein Protein

Machine Learning

Top Venues

PLoS computational biology

Bioinformatics (Oxford, England)

Bioinformatics advances

This page only lists publications with an associated author ORCID identifier.

Publications

Jhih-Siang Lai, Stephen K Burley, Jose M Duarte
ZMPY3D: accelerating protein structure volume analysis through vectorized 3D Zernike moments and Python-based GPU integration. Bioinformatics advances 4 (1) (2024)
Jhih-Siang Lai, Stephen K Burley, Jose M Duarte
ZMPY3D: accelerating protein structure volume analysis through vectorized 3D Zernike moments and Python-based GPU integration. Bioinformatics advances 4 (1) (2024)
Sebastian Bittrich, Joan Segura, Jose M Duarte, Stephen K Burley, Yana Valasatava
RCSB protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments. Bioinformatics (Oxford, England) 40 (6) (2024)
Sebastian Bittrich, Joan Segura, Jose M Duarte, Stephen K Burley, Yana Valasatava
RCSB protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments. Bioinformatics (Oxford, England) 40 (6) (2024)
Jhih-Siang Lai, Stephen K Burley, Jose M Duarte
ZMPY3D: accelerating protein structure volume analysis through vectorized 3D Zernike moments and Python-based GPU integration. Bioinformatics advances 4 (1) (2024)
Sebastian Bittrich, Joan Segura, Jose M Duarte, Stephen K Burley, Yana Valasatava
RCSB protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments. Bioinformatics (Oxford, England) 40 (6) (2024)
Stephen K Burley, Helen M Berman, Jose M Duarte, Zukang Feng, Justin W Flatt, Brian P Hudson, Robert Lowe, Ezra Peisach, Dennis W Piehl, Yana Rose, Andrej Sali, Monica Sekharan, Chenghua Shao, Brinda Vallat, Maria Voigt, John D Westbrook, Jasmine Y Young, Christine Zardecki
Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students. Biomolecules 12 (10) (2022)
Joan Segura, Yana Rose, Sebastian Bittrich, Stephen K Burley, Jose M Duarte
RCSB Protein Data Bank 1D3D module: displaying positional features on macromolecular assemblies. Bioinformatics (Oxford, England) 38 (12) (2022)
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 J 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, Benjamin Webb, John D Westbrook, Shamara Whetstone, Jasmine Y Young, Arthur Zalevsky, Christine Zardecki
RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D. Protein science : a publication of the Protein Society 31 (12) (2022)
Jose M Duarte, Shuchismita Dutta, David S Goodsell, Stephen K Burley
Exploring protein symmetry at the RCSB Protein Data Bank. Emerging topics in life sciences 6 (3) (2022)
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, Yu-He 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 Webb, John D Westbrook, Shamara Whetstone, Jasmine Y Young, Arthur Zalevsky, Christine Zardecki
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 research (2022)
Stephen K Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich, Li Chen, Gregg V Crichlow, Jose M Duarte, Shuchismita Dutta, Maryam Fayazi, Zukang Feng, Justin W Flatt, Sai J Ganesan, David S Goodsell, Sutapa Ghosh, Rachel Kramer Green, Vladimir Guranovic, Jeremy Henry, Brian P Hudson, 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, John D Westbrook, Shamara Whetstone, Jasmine Y Young, Christine Zardecki
RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D. Protein science : a publication of the Protein Society (2021)
Dmytro Guzenko, Stephen K Burley, Jose M Duarte
Real time structural search of the Protein Data Bank. PLoS computational biology 16 (7) (2020)
Aleix Lafita, Spencer E Bliven, Andreas Prlić, Dmytro Guzenko, Peter W Rose, Anthony R Bradley, Paolo Pavan, Douglas Myers-Turnbull, Yana Valasatava, Michael Heuer, Matthew R Larson, Stephen K Burley, Jose M Duarte
BioJava 5: A community driven open-source bioinformatics library. PLoS computational biology 15 (2) (2019)
Dmytro Guzenko, Aleix Lafita, Bohdan Monastyrskyy, Andriy Kryshtafovych, Jose M Duarte
Assessment of protein assembly prediction in CASP13. Proteins 87 (12) (2019)
David S Goodsell, Christine Zardecki, Luigi Di Costanzo, Jose M Duarte, Brian P Hudson, Irina Persikova, Joan Segura, Chenghua Shao, Maria Voigt, John D Westbrook, Jasmine Y Young, Stephen K Burley
RCSB Protein Data Bank: Enabling biomedical research and drug discovery. Protein science : a publication of the Protein Society 29 (1) (2019)
Greg L Hura, Curtis D Hodge, Daniel Rosenberg, Dmytro Guzenko, Jose M Duarte, Bohdan Monastyrskyy, Sergei Grudinin, Andriy Kryshtafovych, John A Tainer, Krzysztof Fidelis, Susan E Tsutakawa
Small angle X-ray scattering-assisted protein structure prediction in CASP13 and emergence of solution structure differences. Proteins 87 (12) (2019)
Spencer E Bliven, Aleix Lafita, Althea Parker, Guido Capitani, Jose M Duarte
Automated evaluation of quaternary structures from protein crystals. PLoS computational biology 14 (4) (2018)
Aleix Lafita, Spencer E Bliven, Andriy Kryshtafovych, Martino Bertoni, Bohdan Monastyrskyy, Jose M Duarte, Torsten Schwede, Guido Capitani
Assessment of protein assembly prediction in CASP12. Proteins (2017)
Anthony R Bradley, Alexander S Rose, Antonín Pavelka, Yana Valasatava, Jose M Duarte, Andreas Prlić, Peter W Rose
MMTF-An efficient file format for the transmission, visualization, and analysis of macromolecular structures. PLoS computational biology 13 (6) (2017)