Chenghua Shao
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View article: Streamlining OneDep Depositions of Multiple Related 3DEM Entries with pdb_extract
Streamlining OneDep Depositions of Multiple Related 3DEM Entries with pdb_extract Open
The Protein Data Bank (PDB) was established in 1971 as the first open-access digital resource in biology with just seven deposited protein structures. Today, the single global PDB archive houses more than 233,000 experimentally determined …
View article: Improving Data Representation of Metalloproteins in the Protein Data Bank
Improving Data Representation of Metalloproteins in the Protein Data Bank Open
The Protein Data Bank (PDB) was established in 1971 as the first open-access digital data resource in biology, initially comprising just seven X- ray crystal structures of proteins. Today, the archive houses more than 225,000 experimentall…
View article: <i>Q</i> -score as a reliability measure for protein, nucleic acid and small-molecule atomic coordinate models derived from 3DEM maps
<i>Q</i> -score as a reliability measure for protein, nucleic acid and small-molecule atomic coordinate models derived from 3DEM maps Open
Atomic coordinate models are important for the interpretation of 3D maps produced with cryoEM and cryoET (3D electron microscopy; 3DEM). In addition to visual inspection of such maps and models, quantitative metrics can inform about the re…
View article: Visualizing and analyzing <scp>3D</scp> biomolecular structures using Mol* at RCSB.org: Influenza A <scp>H5N1</scp> virus proteome case study
Visualizing and analyzing <span>3D</span> biomolecular structures using Mol* at RCSB.org: Influenza A <span>H5N1</span> virus proteome case study Open
The easiest and often most useful way to work with experimentally determined or computationally predicted structures of biomolecules is by viewing their three‐dimensional (3D) shapes using a molecular visualization tool. Mol* was collabora…
View article: Q-score as a reliability measure for protein, nucleic acid, and small molecule atomic coordinate models derived from 3DEM density maps
Q-score as a reliability measure for protein, nucleic acid, and small molecule atomic coordinate models derived from 3DEM density maps Open
Atomic coordinate models are important in the interpretation of 3D maps produced with cryoEM and sub-tomogram averaging in cryoET, or more generically, 3D electron microscopy (3DEM). In addition to visual inspection of such maps and models…
View article: Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank
Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank Open
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, RCSB.org), the US Worldwide Protein Data Bank (wwPDB, wwPDB.org) data center for the global PDB archive, provides access to the PDB data via its RCSB.org…
View article: Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge
Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge Open
The EMDataResource Ligand Model Challenge aimed to assess the reliability and reproducibility of modeling ligands bound to protein and protein-nucleic acid complexes in cryogenic electron microscopy (cryo-EM) maps determined at near-atomic…
View article: EMDB—the Electron Microscopy Data Bank
EMDB—the Electron Microscopy Data Bank Open
The Electron Microscopy Data Bank (EMDB) is the global public archive of three-dimensional electron microscopy (3DEM) maps of biological specimens derived from transmission electron microscopy experiments. As of 2021, EMDB is managed by th…
View article: Assessing and Maximizing the Quality of 3DEM Structure Data at the Worldwide Protein Data Bank
Assessing and Maximizing the Quality of 3DEM Structure Data at the Worldwide Protein Data Bank Open
Journal Article Assessing and Maximizing the Quality of 3DEM Structure Data at the Worldwide Protein Data Bank Get access Justin W Flatt, Justin W Flatt RCSB Protein Data Bank, Rutgers, The State University of New Jersey, New Jersey, Unite…
View article: 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
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 Open
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center for the open-access PDB archive. As wwPDB-designated Archive Keeper, R…
View article: <scp>RCSB</scp> Protein Data bank: Tools for visualizing and understanding biological macromolecules in <scp>3D</scp>
<span>RCSB</span> Protein Data bank: Tools for visualizing and understanding biological macromolecules in <span>3D</span> Open
Now in its 52nd year of continuous operations, the Protein Data Bank (PDB) is the premiere open‐access global archive housing three‐dimensional (3D) biomolecular structure data. It is jointly managed by the Worldwide Protein Data Bank (wwP…
View article: Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students
Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students Open
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the United States National Science Foundation, National Institutes of Health, and Department of Energy, supports structural biologists and Pro…
View article: Assessing PDB macromolecular crystal structure confidence at the individual amino acid residue level
Assessing PDB macromolecular crystal structure confidence at the individual amino acid residue level Open
View article: Assessing macromolecular crystal structures for agreement with experimental data at the individual amino acid residue level
Assessing macromolecular crystal structures for agreement with experimental data at the individual amino acid residue level Open
More than 85% of the atomic-level, three-dimensional (3D) structures of biological macromolecules currently comprising the Protein Data Bank (PDB) archive were determined using macromolecular crystallography (MX).Agreement between atomic c…
View article: Bound! New protein–drug matching card game from the CCDC and PDB-101
Bound! New protein–drug matching card game from the CCDC and PDB-101 Open
Bound! is a card game for students 12 and up where players compete to match the most drugs to their protein targets.The game was created as an educational tool to highlight some structures at the intersection of two databases; the Cambridg…
View article: PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology
PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology Open
View article: <scp>RCSB</scp> Protein Data Bank: Celebrating 50 years of the <scp>PDB</scp> with new tools for understanding and visualizing biological macromolecules in <scp>3D</scp>
<span>RCSB</span> Protein Data Bank: Celebrating 50 years of the <span>PDB</span> with new tools for understanding and visualizing biological macromolecules in <span>3D</span> Open
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the US National Science Foundation, National Institutes of Health, and Department of Energy, has served structural biologists and Protein Data…
View article: Protein Data Bank: 50 Years of Macromolecular Structures Enabling Research and Education
Protein Data Bank: 50 Years of Macromolecular Structures Enabling Research and Education Open
The Protein Data Bank (PDB) was established in 1971 as the first open‐access digital data resource in biology. Beginning with only seven protein structures, the PDB archive has ballooned to >170,000 structures of proteins, DNA, and RNA (to…
View article: Modernized uniform representation of carbohydrate molecules in the Protein Data Bank
Modernized uniform representation of carbohydrate molecules in the Protein Data Bank Open
Since 1971, the Protein Data Bank (PDB) has served as the single global archive for experimentally determined 3D structures of biological macromolecules made freely available to the global community according to the FAIR principles of Find…
View article: 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
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 Open
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), the US data center for the global PDB archive and a founding member of the Worldwide Protein Data Bank partnership, serves tens of thousands of data dep…
View article: D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies
D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies Open
View article: D3R Grand Challenge 4: Blind Prediction of Protein-Ligand Poses, Affinity Rankings, and Relative Binding Free Energies
D3R Grand Challenge 4: Blind Prediction of Protein-Ligand Poses, Affinity Rankings, and Relative Binding Free Energies Open
The Drug Design Data Resource (D3R) aims to identify best practice methods for computer aided drug design through blinded ligand pose prediction and affinity challenges. Herein, we report on the results of Grand Challenge 4 (GC4). GC4 focu…
View article: D3R Grand Challenge 4: Blind Prediction of Protein-Ligand Poses, Affinity Rankings, and Relative Binding Free Energies
D3R Grand Challenge 4: Blind Prediction of Protein-Ligand Poses, Affinity Rankings, and Relative Binding Free Energies Open
The Drug Design Data Resource (D3R) aims to identify best practice methods for computer aided drug design through blinded ligand pose prediction and affinity challenges. Herein, we report on the results of Grand Challenge 4 (GC4). GC4 focu…
View article: RCSB Protein Data Bank: Enabling biomedical research and drug discovery
RCSB Protein Data Bank: Enabling biomedical research and drug discovery Open
Analyses of publicly available structural data reveal interesting insights into the impact of the three‐dimensional (3D) structures of protein targets important for discovery of new drugs (e.g., G‐protein‐coupled receptors, voltage‐gated i…
View article: Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking
Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking Open
View article: Improving Ligand Geometry in Protein Data Bank Structures Computationally
Improving Ligand Geometry in Protein Data Bank Structures Computationally Open
Information about the three‐dimensional structures of complex biological molecules is an indispensable research tool for many fields of study, including biology, chemistry, pharmacology, and computer science. The Protein Data Bank (PDB) is…
View article: Enabling findability, accessibility, interoperability, and reusability with improved data representation of carbohydrates in the Protein Data Bank
Enabling findability, accessibility, interoperability, and reusability with improved data representation of carbohydrates in the Protein Data Bank Open
View article: Outlier analyses of the Protein Data Bank archive using a probability-density-ranking approach
Outlier analyses of the Protein Data Bank archive using a probability-density-ranking approach Open
View article: Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking
Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking Open
1 Summary Docking calculations can be used to accelerate drug discovery by providing predictions of the poses of candidate ligands bound to a targeted protein. However, studies in the literature use varied docking methods, and it is not cl…
View article: Analysis of impact metrics for the Protein Data Bank
Analysis of impact metrics for the Protein Data Bank Open