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Protocol
The Protein Data Bank Archive
Protein Data Bank is the single worldwide archive of experimentally determined macromolecular structure data. Established in 1971 as the first open access data resource in biology, the PDB archive is managed b...
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Article
Open AccessProbabilistic identification of saccharide moieties in biomolecules and their protein complexes
The chemical composition of saccharide complexes underlies their biomedical activities as biomarkers for cardiometabolic disease, various types of cancer, and other conditions. However, because these molecules...
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Protocol
BioMagResBank (BMRB) as a Resource for Structural Biology
The Biological Magnetic Resonance Data Bank (BioMagResBank or BMRB), founded in 1988, serves as the archive for data generated by nuclear magnetic resonance (NMR) spectroscopy of biological systems. NMR spectr...
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Article
Open AccessSolution structure of human myeloid-derived growth factor suggests a conserved function in the endoplasmic reticulum
Human myeloid-derived growth factor (hMYDGF) is a 142-residue protein with a C-terminal endoplasmic reticulum (ER) retention sequence (ERS). Extracellular MYDGF mediates cardiac repair in mice after anoxic inj...
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Article
Backbone resonance assignments and secondary structure of Ebola nucleoprotein 600–739 construct
Ebola viral infections have resulted in several deadly epidemics in recent years in West and Central Africa. Because only one of the seven proteins encoded by the viral genome possesses enzymatic activity, dis...
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Article
Author Correction: Mitochondrial metabolism promotes adaptation to proteotoxic stress
An amendment to this paper has been published and can be accessed via a link at the top of the paper
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Article
Mitochondrial metabolism promotes adaptation to proteotoxic stress
The mechanisms by which cells adapt to proteotoxic stress are largely unknown, but are key to understanding how tumor cells, particularly in vivo, are largely resistant to proteasome inhibitors. Analysis of ca...
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Article
I-PINE web server: an integrative probabilistic NMR assignment system for proteins
Various methods for understanding the structural and dynamic properties of proteins rely on the analysis of their NMR chemical shifts. These methods require the initial assignment of NMR signals to particular ...
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Article
Open AccessAutomated evaluation of consistency within the PubChem Compound database
Identification of discrepant data in aggregated databases is a key step in data curation and remediation. We have applied the ALATIS approach, which is based on the international chemical shift identifier (InC...
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Article
Open AccessNMR-STAR: comprehensive ontology for representing, archiving and exchanging data from nuclear magnetic resonance spectroscopic experiments
The growth of the biological nuclear magnetic resonance (NMR) field and the development of new experimental technology have mandated the revision and enlargement of the NMR-STAR ontology used to represent expe...
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Chapter and Conference Paper
Approach to Improving the Quality of Open Data in the Universe of Small Molecules
We describe an approach to improving the quality and interoperability of open data related to small molecules, such as metabolites, drugs, natural products, food additives, and environmental contaminants. The ...
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Protocol
Tools for Enhanced NMR-Based Metabolomics Analysis
Metabolomics is the study of profiles of small molecules in biological fluids, cells, or organs. These profiles can be thought of as the “fingerprints” left behind from chemical processes occurring in biologic...
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Book
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Chapter
View from Nuclear Magnetic Resonance Spectroscopy
Nuclear magnetic resonance (NMR) spectroscopy is one of the three major approaches for determining the structures of biological macromolecules. Historically, NMR spectroscopy was number two after X-ray crystal...
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Chapter
Current Solution NMR Techniques for Structure-Function Studies of Proteins and RNA Molecules
We briefly review current technology for structure-function investigations of biological macromolecules in solution by nuclear magnetic resonance spectroscopy, which enable hybrid methods. An advantage of NMR ...
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Article
Open AccessUnique identifiers for small molecules enable rigorous labeling of their atoms
Rigorous characterization of small organic molecules in terms of their structural and biological properties is vital to biomedical research. The three-dimensional structure of a molecule, its ‘photo ID’, is in...
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Protocol
Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive
The Protein Data Bank (PDB)––the single global repository of experimentally determined 3D structures of biological macromolecules and their complexes––was established in 1971, becoming the first open-access di...
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Article
Open AccessThe AUDANA algorithm for automated protein 3D structure determination from NMR NOE data
We introduce AUDANA (Automated Database-Assisted NOE Assignment), an algorithm for determining three-dimensional structures of proteins from NMR data that automates the assignment of 3D-NOE spectra, generates ...
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Article
Open AccessPublication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins
The nuclear magnetic resonance (NMR) spectroscopic data for biological macromolecules archived at the BioMagResBank (BMRB) provide a rich resource of biophysical information at atomic resolution. The NMR data ...
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Article
Open AccessIntegrative NMR for biomolecular research
NMR spectroscopy is a powerful technique for determining structural and functional features of biomolecules in physiological solution as well as for observing their intermolecular interactions in real-time. Ho...
