ArticleNucleic acids research2016
PDBFlex: exploring flexibility in protein structures.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
40 citing papers in PubMed.
- Disentangling coevolutionary constraints for modeling protein conformational heterogeneity.Communications chemistry · 2026Article
- Sequence-based calculation of local energetic frustration in proteins.Structural dynamics (Melville, N.Y.) · 2025Article
- MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model.Briefings in bioinformatics · 2025Article
- Beyond static structures: protein dynamic conformations modeling in the post-AlphaFold era.Briefings in bioinformatics · 2025Review
- Dissecting Uricase Immunogenicity: Unveiling the Role of Quaternary Epitopes through In Silico Analysis : Quaternary Epitope Insights in Uricase Immunogenicity.Galen medical journal · 2025Article
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- Targeting Efficient Features of Urate Oxidase to Increase Its Solubility.Applied biochemistry and biotechnology · 2024Article
- Sequence, Structure, and Functional Space of Drosophila De Novo Proteins.Genome biology and evolution · 2024Article
- A dataset of alternately located segments in protein crystal structures.Scientific data · 2024Article
- 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.Nucleic acids research · 2023Article
- IRAA: A statistical tool for investigating a protein-protein interaction interface from multiple structures.Protein science : a publication of the Protein Society · 2023Article
- RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D.Protein science : a publication of the Protein Society · 2022Article
- Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students.Biomolecules · 2022Review
- What the protein data bank tells us about the evolutionary conservation of protein conformational diversity.Protein science : a publication of the Protein Society · 2022Article
- D3PM: a comprehensive database for protein motions ranging from residue to domain.BMC bioinformatics · 2022Article
- Theta-Defensins to Counter COVID-19 as Furin Inhibitors:Computational and mathematical methods in medicine · 2022Article
- ModFlex: Towards Function Focused Protein Modeling.Journal of molecular biology · 2021Article
- Bioinformatic analysis of subfamily-specific regions in 3D-structures of homologs to study functional diversity and conformational plasticity in protein superfamilies.Computational and structural biotechnology journal · 2021Article
- The Active Site of a Prototypical "Rigid" Drug Target is Marked by Extensive Conformational Dynamics.Angewandte Chemie (International ed. in English) · 2020Article
- High-resolution structures of the SARS-CoV-2 2'-Science signaling · 2020Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
The PDBFlex database, available freely and with no login requirements at http://pdbflex.org, provides information on flexibility of protein structures as revealed by the analysis of variations between depositions of different structural models of the same protein in the Protein Data Bank (PDB). PDBFlex collects information on all instances of such depositions, identifying them by a 95% sequence identity threshold, performs analysis of their structural differences and clusters them according to their structural similarities for easy analysis. The PDBFlex contains tools and viewers enabling in-depth examination of structural variability including: 2D-scaling visualization of RMSD distances between structures of the same protein, graphs of average local RMSD in the aligned structures of protein chains, graphical presentation of differences in secondary structure and observed structural disorder (unresolved residues), difference distance maps between all sets of coordinates and 3D views of individual structures and simulated transitions between different conformations, the latter displayed using JSMol visualization software.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.