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Stephen K. Burley
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2020 – today
- 2024
- [j25]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) - [j24]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): 100931 (2024) - 2023
- [j23]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) - [j22]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): 488-508 (2023) - 2022
- [j21]Valérie de Crécy-Lagard
, Rocio Amorin de Hegedus
, Cecilia N. Arighi
, Jill Babor, Alex Bateman
, Ian Blaby
, Crysten Blaby-Haas, Alan J. 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 S. 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) - [j20]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): 1452-1454 (2022) - [j19]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): 3304-3305 (2022) - 2021
- [j18]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): 5526-5527 (2021) - [j17]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): D437-D451 (2021) - [j16]David Sehnal
, Sebastian Bittrich
, Mandar S. Deshpande
, Radka Svobodová Vareková
, 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): 431-437 (2021) - 2020
- [j15]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: 25 (2020) - [j14]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): 99-119 (2020) - [j13]Dmytro Guzenko, Stephen K. Burley, Jose M. Duarte:
Real time structural search of the Protein Data Bank. PLoS Comput. Biol. 16(7) (2020) - [j12]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) - [j11]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)
2010 – 2019
- 2019
- [j10]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): 1-18 (2019) - [j9]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): D464-D474 (2019) - [j8]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) - 2018
- [j7]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: bay002 (2018) - [j6]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): 1-20 (2018) - [c1]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: 29-33 - 2017
- [j5]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): D271-D281 (2017) - 2016
- [j4]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): 3833-3835 (2016) - [j3]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): 651-668 (2016) - 2015
- [j2]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): 345-356 (2015) - 2011
- [j1]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): 465-474 (2011)
Coauthor Index
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last updated on 2024-08-05 21:13 CEST by the dblp team
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