John L. Markley

19 papers Misc 1Journal 15Unranked 3
YearRankTypeTitle / Venue / Authors
2021 J jnl
CHESPA/CHESCA-SPARKY: automated NMR data analysis plugins for SPARKY to map protein allostery.
Bioinform.
Hongzhao Shao, Stephen Boulton, Cristina Olivieri, Hebatallah Mohamed, Madoka Akimoto, Manu Veliparambil Subrahmanian, Gianluigi Veglia, John L. Markley, Giuseppe Melacini, Woonghee Lee
2021 — conf
PyBMRB: Data visualization tool for BioMagResBank.
SciPy
Kumaran Baskaran, Jonathan R. Wedell, Eldon L. Ulrich, Jeffery C. Hoch, John L. Markley
2020 J jnl
PISA-SPARKY: an interactive SPARKY plugin to analyze oriented solid-state NMR spectra of helical membrane proteins.
Bioinform.
Daniel K. Weber, Songlin Wang, John L. Markley, Gianluigi Veglia, Woonghee Lee
2019 — conf
Approach to Improving the Quality of Open Data in the Universe of Small Molecules.
BIS (Workshops)
John L. Markley, Hesam Dashti, Jonathan R. Wedell, William M. Westler, Eldon L. Ulrich, Hamid R. Eghbalnia
2018 J jnl
PINE-SPARKY.2 for automated NMR-based protein structure research.
Bioinform.
Woonghee Lee, John L. Markley
2018 J jnl
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data.
Database J. Biol. Databases Curation
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
2016 J jnl
Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins.
J. Biomed. Semant.
Masashi Yokochi, Naohiro Kobayashi, Eldon L. Ulrich, Akira R. Kinjo, Takeshi Iwata, Yannis E. Ioannidis, Miron Livny, John L. Markley, Haruki Nakamura, Chojiro Kojima, Toshimichi Fujiwara
2015 J jnl
NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy.
Bioinform.
Woonghee Lee, Marco Tonelli, John L. Markley
2014 J jnl
The Protein Data Bank archive as an open data resource.
J. Comput. Aided Mol. Des.
Helen M. Berman, Gerard J. Kleywegt, Haruki Nakamura, John L. Markley
2013 J jnl
ADAPT-NMR Enhancer: complete package for reduced dimensionality in protein NMR spectroscopy.
Bioinform.
Woonghee Lee, Arash Bahrami, John L. Markley
2012 J jnl
NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB.
Nucleic Acids Res.
Jurgen F. Doreleijers, Wim F. Vranken, Christopher F. Schulte, John L. Markley, Eldon L. Ulrich, Gert Vriend, Geerten W. Vuister
2012 — conf
PACSY database, a relational database management system for Protein structure and nuclear Magnetic Resonance chemical shift analysis.
BIBM Workshops
Woonghee Lee, John L. Markley
2011 J jnl
PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination.
Bioinform.
Woonghee Lee, Jin Hae Kim, William M. Westler, John L. Markley
2009 J jnl
PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy.
Bioinform.
Woonghee Lee, William M. Westler, Arash Bahrami, Hamid Eghbalnia, John L. Markley
2009 J jnl
Probabilistic Interaction Network of Evidence Algorithm and its Application to Complete Labeling of Peak Lists from Protein NMR Spectroscopy.
PLoS Comput. Biol.
Arash Bahrami, Amir H. Assadi, John L. Markley, Hamid Eghbalnia
2008 J jnl
BioMagResBank.
Nucleic Acids Res.
Eldon L. Ulrich, Hideo Akutsu, Jurgen F. Doreleijers, Yoko Harano, Yannis E. Ioannidis, Jundong Lin, Miron Livny, Steve Mading, Dimitri Maziuk, Zachary Miller, Eiichi Nakatani, Christopher F. Schulte, David E. Tolmie, R. Kent Wenger, Hongyang Yao, John L. Markley
2008 J jnl
Remediation of the protein data bank archive.
Nucleic Acids Res.
Kim Henrick, Zukang Feng, Wolfgang Bluhm, Dimitris Dimitropoulos, Jurgen F. Doreleijers, Shuchismita Dutta, Judith L. Flippen-Anderson, John M. C. Ionides, Chisa Kamada, Eugene Krissinel, Catherine L. Lawson, John L. Markley, Haruki Nakamura, Richard H. Newman, Yukiko Shimizu, Jawahar Swaminathan, Sameer Velankar, Jeramia Ory, Eldon L. Ulrich, Wim F. Vranken, John D. Westbrook, Reiko Yamashita, Huanwang Yang, Jasmine Young, Muhammed Yousufuddin, Helen M. Berman
2007 Misc conf
New Bioinformatics Resources For Metabolomics.
Pacific Symposium on Biocomputing
John L. Markley, Mark E. Anderson, Qiu Cui, Hamid Eghbalnia, Ian A. Lewis, Adrian D. Hegeman, Jing Li, Christopher F. Schulte, Michael R. Sussman, William M. Westler, Eldon L. Ulrich, Zsolt Zolnai
2007 J jnl
The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data.
Nucleic Acids Res.
Helen M. Berman, Kim Henrick, Haruki Nakamura, John L. Markley