Stephen K. Burley

Publication Activity (10 Years)

Years Active: 2011-2024
Publications (10 Years): 24

Top Topics

Protein Data Bank

Grand Challenge

Structural Information

Top Venues

Nucleic Acids Res.

J. Comput. Aided Mol. Des.

PLoS Comput. Biol.

Publications

Preeti Choudhary, Zukang Feng, John M. Berrisford, Henry Chao, Yasuyo Ikegawa, Ezra Peisach, Dennis W. Piehl, James Smith, Ahsan Tanweer, Mihaly Varadi, John D. Westbrook, Jasmine Young, Ardan Patwardhan, Kyle L. Morris, Jeffrey C. Hoch, Genji Kurisu, Sameer Velankar, Stephen K. Burley
PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank. Database J. Biol. Databases Curation 2024 (2024)
David S. Goodsell, Shuchismita Dutta, Brian P. Hudson, Maria Voigt, Stephen K. Burley, Christine Zardecki
Folding paper models of biostructures for outreach and education. Patterns 5 (2) (2024)
Joan Segura, Yana Rose, Chunxiao Bi, Jose M. Duarte, Stephen K. Burley, Sebastian Bittrich
RCSB Protein Data Bank: visualizing groups of experimentally determined PDB structures alongside computed structure models of proteins. Frontiers Bioinform. 3 (2023)
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
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. 51 (D1) (2023)
Sebastian Bittrich, Yana Rose, Joan Segura, Robert Lowe, John D. Westbrook, Jose M. Duarte, Stephen K. Burley
RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB. Bioinform. 38 (5) (2022)
Valérie de Crécy-Lagard, Rocio Amorin de Hegedus, Cecilia N. Arighi, Jill Babor, Alex Bateman, Ian Blaby, Crysten Blaby-Haas, Alan Bridge, Stephen K. Burley, Stacey Cleveland, Lucy J. Colwell, Ana Conesa, Christian Dallago, Antoine Danchin, Anita de Waard, Adam Deutschbauer, Raquel Dias, Yousong Ding, Gang Fang, Iddo Friedberg, John Gerlt, Joshua Goldford, Mark Gorelik, Benjamin M. Gyori, Christopher Henry, Geoffrey Hutinet, Marshall Jaroch, Peter D. Karp, Liudmyla Kondratova, Zhiyong Lu, Aron Marchler-Bauer, Maria Jesus Martin, Claire D. McWhite, Gaurav D. Moghe, Paul Monaghan, Anne Morgat, Christopher J. Mungall, Darren A. Natale, William C. Nelson, Seán I. O'Donoghue, Christine A. Orengo, Katherine H. O'Toole, Predrag Radivojac, Colbie Reed, Richard J. Roberts, Dmitri Rodionov, Irina A. Rodionova, Jeffrey DePons, Lana Saleh, Gloria M. Sheynkman, Françoise Thibaud-Nissen, Paul D. Thomas, Peter Uetz, David Vallenet, Erica Watson Carter, Peter Weigele, Valerie Wood, Elisha M. Wood-Charlson, Jin Xu
A roadmap for the functional annotation of protein families: a community perspective. Database J. Biol. Databases Curation 2022 (2022) (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. Bioinform. 38 (12) (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)
Joan Segura, Yana Rose, John D. Westbrook, Stephen K. Burley, Jose M. Duarte
RCSB Protein Data Bank 1D tools and services. Bioinform. 36 (22-23) (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)
Dmytro Guzenko, Stephen K. Burley, Jose M. Duarte
Real time structural search of the Protein Data Bank. PLoS Comput. Biol. 16 (7) (2020)
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)
Zukang Feng, Natalie Verdiguel, Luigi Di Costanzo, David S. Goodsell, John D. Westbrook, Stephen K. Burley, Christine Zardecki
Impact of the Protein Data Bank Across Scientific Disciplines. Data Sci. J. 19 (2020)
Conor D. Parks, Zied Gaieb, Michael Chiu, Huanwang Yang, Chenghua Shao, W. Patrick Walters, Johanna M. Jansen, Georgia B. McGaughey, Richard A. Lewis, Scott D. Bembenek, Michael K. Ameriks, Tara Mirzadegan, Stephen K. Burley, Rommie E. Amaro, Michael K. Gilson
D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. J. Comput. Aided Mol. Des. 34 (2) (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)
Zied Gaieb, Conor D. Parks, Michael Chiu, Huanwang Yang, Chenghua Shao, W. Patrick Walters, Millard H. Lambert, Neysa Nevins, Scott D. Bembenek, Michael K. Ameriks, Tara Mirzadegan, Stephen K. Burley, Rommie E. Amaro, Michael K. Gilson
D3R Grand Challenge 3: blind prediction of protein-ligand poses and affinity rankings. J. Comput. Aided Mol. Des. 33 (1) (2019)
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
BioJava 5: A community driven open-source bioinformatics library. PLoS Comput. Biol. 15 (2) (2019)
Zied Gaieb, Shuai Liu, Symon Gathiaka, Michael Chiu, Huanwang Yang, Chenghua Shao, Victoria A. Feher, W. Patrick Walters, Bernd Kuhn, Markus G. Rudolph, Stephen K. Burley, Michael K. Gilson, Rommie E. Amaro
D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. J. Comput. Aided Mol. Des. 32 (1) (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)
Jasmine Young, John D. Westbrook, Zukang Feng, Ezra Peisach, Irina Persikova, Raul Sala, Sanchayita Sen, John M. Berrisford, Jawahar Swaminathan, Thomas J. Oldfield, Aleksandras Gutmanas, Reiko Igarashi, David R. Armstrong, Kumaran Baskaran, Li Chen, Minyu Chen, Alice R. Clark, Luigi Di Costanzo, Dimitris Dimitropoulos, Guanghua Gao, Sutapa Ghosh, Swanand P. Gore, Vladimir Guranovic, Pieter M. S. Hendrickx, Brian P. Hudson, Yasuyo Ikegawa, Yumiko Kengaku, Catherine L. Lawson, Yuhe Liang, Lora Mak, Abhik Mukhopadhyay, Buvaneswari Coimbatore Narayanan, Kayoko Nishiyama, Ardan Patwardhan, Gaurav Sahni, Eduardo Sanz-García, Junko Sato, Monica Sekharan, Chenghua Shao, Oliver S. Smart, Lihua Tan, Glen van Ginkel, Huanwang Yang, Marina Zhuravleva, John L. Markley, Haruki Nakamura, Genji Kurisu, Gerard J. Kleywegt, Sameer Velankar, Helen M. Berman, Stephen K. Burley
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data. Database J. Biol. Databases Curation 2018 (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)
Andreas Prlic, Tara Kalro, Roshni Bhattacharya, Cole H. Christie, Stephen K. Burley, Peter W. Rose
Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank. Bioinform. 32 (24) (2016)
Symon Gathiaka, Shuai Liu, Michael Chiu, Huanwang Yang, Jeanne A. Stuckey, You-Na Kang, Jim Delproposto, Ginger Kubish, James B. Dunbar Jr., Heather A. Carlson, Stephen K. Burley, W. Patrick Walters, Rommie E. Amaro, Victoria A. Feher, Michael K. Gilson
D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions. J. Comput. Aided Mol. Des. 30 (9) (2016)
Peter W. Rose, Andreas Prlic, Chunxiao Bi, Wolfgang Bluhm, Cole H. Christie, Shuchismita Dutta, Rachel Kramer Green, David S. Goodsell, John D. Westbrook, Jesse Woo, Jasmine Young, Christine Zardecki, Helen M. Berman, Philip E. Bourne, Stephen K. Burley
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. Nucleic Acids Res. 43 (Database-Issue) (2015)
Ursula Pieper, Benjamin M. Webb, David T. Barkan, Dina Schneidman-Duhovny, Avner Schlessinger, Hannes Braberg, Zheng Yang, Elaine C. Meng, Eric F. Pettersen, Conrad C. Huang, Ruchira S. Datta, Parthasarathy Sampathkumar, Mallur S. Madhusudhan, Kimmen Sjölander, Thomas E. Ferrin, Stephen K. Burley, Andrej Sali
ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 39 (Database-Issue) (2011)