New Bioinformatics Resources For Metabolomics. - John L. Markley; Mark E. Anderson 001; 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 (Pacific Symposium on Biocomputing, 2007)

The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. - Helen M. Berman; Kim Henrick; Haruki Nakamura; John L. Markley (Nucleic Acids Res., 2007)

Remediation of the protein data bank archive. - 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; et al. (Nucleic Acids Res., 2008)

BioMagResBank. - 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; et al. (Nucleic Acids Res., 2008)

PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy. - Woonghee Lee 003; William M. Westler; Arash Bahrami; Hamid Eghbalnia; John L. Markley (Bioinform., 2009)

Probabilistic Interaction Network of Evidence Algorithm and its Application to Complete Labeling of Peak Lists from Protein NMR Spectroscopy. - Arash Bahrami; Amir H. Assadi; John L. Markley; Hamid Eghbalnia (PLoS Comput. Biol., 2009)

PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination. - Woonghee Lee 003; Jin Hae Kim; William M. Westler; John L. Markley (Bioinform., 2011)

PACSY database, a relational database management system for Protein structure and nuclear Magnetic Resonance chemical shift analysis. - Woonghee Lee 003; John L. Markley (BIBM Workshops, 2012)

NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB. - Jurgen F. Doreleijers; Wim F. Vranken; Christopher F. Schulte; John L. Markley; Eldon L. Ulrich; Gert Vriend; Geerten W. Vuister (Nucleic Acids Res., 2012)

ADAPT-NMR Enhancer: complete package for reduced dimensionality in protein NMR spectroscopy. - Woonghee Lee 003; Arash Bahrami; John L. Markley (Bioinform., 2013)

The Protein Data Bank archive as an open data resource. - Helen M. Berman; Gerard J. Kleywegt; Haruki Nakamura; John L. Markley (J. Comput. Aided Mol. Des., 2014)

NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. - Woonghee Lee 003; Marco Tonelli; John L. Markley (Bioinform., 2015)

Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins. - 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 (J. Biomed. Semant., 2016)

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data. - 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; et al. (Database J. Biol. Databases Curation, 2018)

PINE-SPARKY.2 for automated NMR-based protein structure research. - Woonghee Lee 003; John L. Markley (Bioinform., 2018)

Approach to Improving the Quality of Open Data in the Universe of Small Molecules. - John L. Markley; Hesam Dashti; Jonathan R. Wedell; William M. Westler; Eldon L. Ulrich; Hamid R. Eghbalnia (BIS (Workshops), 2019)

PISA-SPARKY: an interactive SPARKY plugin to analyze oriented solid-state NMR spectra of helical membrane proteins. - Daniel K. Weber; Songlin Wang; John L. Markley; Gianluigi Veglia; Woonghee Lee 003 (Bioinform., 2020)

PyBMRB: Data visualization tool for BioMagResBank. - Kumaran Baskaran; Jonathan R. Wedell; Eldon L. Ulrich; Jeffery C. Hoch; John L. Markley (SciPy, 2021)

CHESPA/CHESCA-SPARKY: automated NMR data analysis plugins for SPARKY to map protein allostery. - Hongzhao Shao; Stephen Boulton; Cristina Olivieri; Hebatallah Mohamed; Madoka Akimoto; Manu Veliparambil Subrahmanian; Gianluigi Veglia; John L. Markley; Giuseppe Melacini; Woonghee Lee 003 (Bioinform., 2021)