Peter W. Rose

Publication Activity (10 Years)

Years Active: 1999-2023
Publications (10 Years): 19

Top Topics

Protein Data Bank

Top Venues

PLoS Comput. Biol.

Nucleic Acids Res.

Publications

John H. Morris, Karthik Soman, Rabia E. Akbas, Xiaoyuan Zhou, Brett Smith, Elaine C. Meng, Conrad C. Huang, Gabriel Cerono, Gundolf Schenk, Angela Rizk-Jackson, Adil Harroud, Lauren M. Sanders, Sylvain V. Costes, Krish Bharat, Arjun Chakraborty, Alexander R. Pico, Taline Mardirossian, Michael J. Keiser, Alice Tang, Josef Hardi, Yongmei Shi, Mark A. Musen, Sharat Israni, Sui Huang, Peter W. Rose, Charlotte A. Nelson, Sergio E. Baranzini
The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information. Bioinform. 39 (2) (2023)
Mary P. Thomas, Andreas W. Götz, Martin C. Kandes, Mai H. Nguyen, Paul Rodríguez, Peter W. Rose, Robert S. Sinkovits
Developing a Best Practices Training Program in Cyberinfrastructure-Enabled Machine Learning Research. PEARC (2023)
Karthik Soman, Peter W. Rose, John H. Morris, Rabia E. Akbas, Brett Smith, Braian Peetoom, Catalina Villouta-Reyes, Gabriel Cerono, Yongmei Shi, Angela Rizk-Jackson, Sharat Israni, Charlotte A. Nelson, Sui Huang, Sergio E. Baranzini
Biomedical knowledge graph-enhanced prompt generation for large language models. CoRR (2023)
Daniel K. Gehlhaar, Brock A. Luty, Philip P. Cheung, Andy H. Litman, Robert M. Owen, Peter W. Rose
The Pfizer Crystal Structure Database: An essential tool for structure-based design at Pfizer. J. Comput. Chem. 43 (15) (2022)
Sergio E. Baranzini, Katy Börner, John Morris, Charlotte A. Nelson, Karthik Soman, Erica Schleimer, Michael J. Keiser, Mark A. Musen, Roger Pearce, Tahsin Reza, Brett Smith, Bruce William Herr II, Boris Oskotsky, Angela Rizk-Jackson, Katherine P. Rankin, Stephan J. Sanders, Riley Bove, Peter W. Rose, Sharat Israni, Sui Huang
A Biomedical Open Knowledge Network Harnesses the Power of AI to Understand Deep Human Biology. AI Mag. 43 (1) (2022)
Shiqiang Tao, Wei-Chun Chou, Jianfu Li, Jingcheng Du, Pritham Ram, Rashmie Abeysinghe, Hua Xu, Xiaoqian Jiang, Peter W. Rose, Lucila Ohno-Machado, Guo-Qiang Zhang
IMI-CDE: an interactive interface for collaborative mapping of study variables to common data elements. ICHI (2022)
Faryad Sahneh, Meghan A. Balk, Marina Kisley, Chi-Kwan Chan, Mercury Fox, Brian Nord, Eric Lyons, Tyson Swetnam, Daniela Huppenkothen, Will Sutherland, Ramona L. Walls, Daven P. Quinn, Tonantzin Tarin, David S. LeBauer, David Ribes, Dunbar P. Birnie III, Carol Lushbough, Eric Carr, Grey Nearing, Jeremy Fischer, Kevin Tyle, Luis Carrasco, Meagan Lang, Peter W. Rose, Richard R. Rushforth, Samapriya Roy, Thomas Matheson, Tina Lee, C. Titus Brown, Tracy K. Teal, Monica Papes, Stephen G. Kobourov, Nirav C. Merchant
Ten simple rules to cultivate transdisciplinary collaboration in data science. PLoS Comput. Biol. 17 (5) (2021)
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)
Spencer E. Bliven, Aleix Lafita, Peter W. Rose, Guido Capitani, Andreas Prlic, Philip E. Bourne
Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm. PLoS Comput. Biol. 15 (4) (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)
Adam Rule, Amanda Birmingham, Cristal Zuniga, Ilkay Altintas, Shih-Cheng Huang, Rob Knight, Niema Moshiri, Mai H. Nguyen, Sara Brin Rosenthal, Fernando Pérez, Peter W. Rose
Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks. PLoS Comput. Biol. 15 (7) (2019)
Alexander S. Rose, Anthony R. Bradley, Yana Valasatava, Jose M. Duarte, Andreas Prlic, Peter W. Rose
NGL viewer: web-based molecular graphics for large complexes. Bioinform. 34 (21) (2018)
Adam Rule, Amanda Birmingham, Cristal Zuniga, Ilkay Altintas, Shih-Cheng Huang, Rob Knight, Niema Moshiri, Mai H. Nguyen, Sara Brin Rosenthal, Fernando Pérez, Peter W. Rose
Ten Simple Rules for Reproducible Research in Jupyter Notebooks. CoRR (2018)
Brock A. Luty, Peter W. Rose
The need for scientific software engineering in the pharmaceutical industry. J. Comput. Aided Mol. Des. 31 (3) (2017)
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)
Jianjiong Gao, Andreas Prlic, Chunxiao Bi, Wolfgang Bluhm, Dimitris Dimitropoulos, Dong Xu, Philip E. Bourne, Peter W. Rose
BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank. Bioinform. 33 (13) (2017)
Anthony R. Bradley, Alexander S. Rose, Antonín Pavelka, Yana Valasatava, Jose M. Duarte, Andreas Prlic, Peter W. Rose
MMTF - An efficient file format for the transmission, visualization, and analysis of macromolecular structures. PLoS Comput. Biol. 13 (6) (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)
Alexander S. Rose, Anthony R. Bradley, Yana Valasatava, Jose M. Duarte, Andreas Prlic, Peter W. Rose
Web-based molecular graphics for large complexes. Web3D (2016)
Gregory B. Quinn, Chunxiao Bi, Cole H. Christie, Kyle Pang, Andreas Prlic, Takanori Nakane, Christine Zardecki, Maria Voigt, Helen M. Berman, Philip E. Bourne, Peter W. Rose
: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank. Bioinform. 31 (1) (2015)
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)
Peter W. Rose, Chunxiao Bi, Wolfgang Bluhm, Cole H. Christie, Dimitris Dimitropoulos, Shuchismita Dutta, Rachel Kramer Green, David S. Goodsell, Andreas Prlic, Martha Quesada, Greg B. Quinn, Alexander G. Ramos, John D. Westbrook, Jasmine Young, Christine Zardecki, Helen M. Berman, Philip E. Bourne
The RCSB Protein Data Bank: new resources for research and education. Nucleic Acids Res. 41 (Database-Issue) (2013)
Andreas Prlic, Andrew D. Yates, Spencer Bliven, Peter W. Rose, Julius O. B. Jacobsen, Peter V. Troshin, Mark Chapman, Jianjiong Gao, Chuan Hock Koh, Sylvain Foisy, Richard C. G. Holland, Gediminas Rimsa, Michael L. Heuer, Hannes Brandstätter-Müller, Philip E. Bourne, Scooter Willis
BioJava: an open-source framework for bioinformatics in 2012. Bioinform. 28 (20) (2012)
Wolfgang Bluhm, Bojan Beran, Chunxiao Bi, Dimitris Dimitropoulos, Andreas Prlic, Greg B. Quinn, Peter W. Rose, Chaitali Shah, Jasmine Young, Benjamin T. Yukich, Helen M. Berman, Philip E. Bourne
Quality assurance for the query and distribution systems of the RCSB Protein Data Bank. Database J. Biol. Databases Curation 2011 (2011)
Peter W. Rose, Bojan Beran, Chunxiao Bi, Wolfgang Bluhm, Dimitris Dimitropoulos, David S. Goodsell, Andreas Prlic, Martha Quesada, Greg B. Quinn, John D. Westbrook, Jasmine Young, Benjamin T. Yukich, Christine Zardecki, Helen M. Berman, Philip E. Bourne
The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res. 39 (Database-Issue) (2011)
Andreas Prlic, Marco A. Martinez, Dimitris Dimitropoulos, Bojan Beran, Benjamin T. Yukich, Peter W. Rose, Philip E. Bourne, J. Lynn Fink
Integration of open access literature into the RCSB Protein Data Bank using BioLit. BMC Bioinform. 11 (2010)
Philip E. Bourne, Bojan Beran, Chunxiao Bi, Wolfgang Bluhm, Roland L. Dunbrack Jr., Andreas Prlic, Greg B. Quinn, Peter W. Rose, Raship Shah, Wendy Tao, Brian D. Weitzner, Benjamin T. Yukich
Will Widgets and Semantic Tagging Change Computational Biology? PLoS Comput. Biol. 6 (2) (2010)
Andreas Prlic, Spencer Bliven, Peter W. Rose, Wolfgang Bluhm, Chris Bizon, Adam Godzik, Philip E. Bourne
Pre-calculated protein structure alignments at the RCSB PDB website. Bioinform. 26 (23) (2010)
Gennady Verkhivker, Djamal Bouzida, Daniel K. Gehlhaar, Paul A. Rejto, Sandra Arthurs, Anthony B. Colson, Stephan T. Freer, Veda Larson, Brock A. Luty, Tami Marrone, Peter W. Rose
Deciphering common failures in molecular docking of ligand-protein complexes. J. Comput. Aided Mol. Des. 14 (8) (2000)
Djamal Bouzida, Sandra Arthurs, Anthony B. Colson, Stephan T. Freer, Daniel K. Gehlhaar, Veda Larson, Brock A. Luty, Paul A. Rejto, Peter W. Rose, Gennady Verkhivker
Thermodynamics and Kinetics of Ligand-Protein Binding Studied with the Weighted Histogram Analysis Method and Simulated Annealing. Pacific Symposium on Biocomputing (1999)