-
1
Revisiting Chameleon Sequences in the Protein Data Bank
Published 2018-07-01Subjects: Get full text
Article -
2
Disordered Residues and Patterns in the Protein Data Bank
Published 2020-03-01“…We created a new library of disordered patterns and disordered residues in the Protein Data Bank (PDB). To obtain such datasets, we clustered the PDB and obtained the groups of chains with different identities and marked disordered residues. …”
Get full text
Article -
3
Impact of the Protein Data Bank Across Scientific Disciplines
Published 2020-06-01“…The Protein Data Bank archive (PDB) was established in 1971 as the 1st open access digital data resource for biology and medicine. …”
Get full text
Article -
4
Real time structural search of the Protein Data Bank.
Published 2020-07-01“…This fact, together with recent growth of oligomeric structures in the Protein Data Bank (PDB), demands more efficient approaches to oligomeric assembly alignment/retrieval. …”
Get full text
Article -
5
Quantifying and comparing radiation damage in the Protein Data Bank
Published 2022-03-01“…Here, the AUs introduce the B net metric, a single value summarising the extent of radiation damage of a protein crystal structure, and use B net to detect radiation damage in structures deposited in the Protein Data Bank.…”
Get full text
Article -
6
Exploring the universe of protein structures beyond the Protein Data Bank.
Published 2010-01-01“…It is currently believed that the atlas of existing protein structures is faithfully represented in the Protein Data Bank. However, whether this atlas covers the full universe of all possible protein structures is still a highly debated issue. …”
Get full text
Article -
7
Identification of Intrinsic Disorder in Complexes from the Protein Data Bank
Published 2020-07-01Get full text
Article -
8
Trends in coordination of rhenium organometallic complexes in the Protein Data Bank
Published 2022-03-01“…This topical review is focused on the development of radiopharmaceuticals containing the radioisotopes of rhenium and technetium and, therefore, on the occurrence of these organometallic complexes in protein structures in the Worldwide Protein Data Bank (wwPDB). The purpose of incorporating the group 7 transition metals of rhenium/technetium in the protein and the reasons for study by protein crystallography are described, as certain PDB studies were not aimed at drug development. …”
Get full text
Article -
9
Interesting structures: education and outreach at the RCSB Protein Data Bank.
Published 2008-05-01Get full text
Article -
10
Mining the Protein Data Bank to inspire fragment library design
Published 2023-02-01“…In this study, we searched the Protein Data Bank for fragments with multiple binding modes and targeting different sites. …”
Get full text
Article -
11
Properties of Cavities in Biological Structures—A Survey of the Protein Data Bank
Published 2020-11-01Get full text
Article -
12
Disordered patterns in clustered Protein Data Bank and in eukaryotic and bacterial proteomes.
Published 2011-01-01“…We have constructed the clustered Protein Data Bank and obtained clusters of chains of different identity inside each cluster, http://bioinfo.protres.ru/st_pdb/. …”
Get full text
Article -
13
A new generation of crystallographic validation tools for the protein data bank.
Published 2011“…This report presents the conclusions of the X-ray Validation Task Force of the worldwide Protein Data Bank (PDB). The PDB has expanded massively since current criteria for validation of deposited structures were adopted, allowing a much more sophisticated understanding of all the components of macromolecular crystals. …”
Journal article -
14
Atomic Motif Recognition in (Bio)Polymers: Benchmarks From the Protein Data Bank
Published 2019-04-01“…Here we discuss how unsupervised machine learning schemes can be used to recognize patterns based exclusively on the frequency with which different motifs occur, taking high-resolution structures from the Protein Data Bank as benchmarks. We first discuss the application of a density-based motif recognition scheme in combination with traditional representations of protein structure (namely, interatomic distances and backbone dihedrals). …”
Get full text
Article -
15
Mining the Protein Data Bank to improve prediction of changes in protein-protein binding
Published 2021-01-01“…Given the ongoing growth of near-redundant structures in the Protein Data Bank, our method will only increase in applicability and accuracy.…”
Get full text
Article -
16
Mining the Protein Data Bank to improve prediction of changes in protein-protein binding.
Published 2021-01-01“…Given the ongoing growth of near-redundant structures in the Protein Data Bank, our method will only increase in applicability and accuracy.…”
Get full text
Article -
17
Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data
Published 2023-12-01“…Abstract Macromolecular complexes are essential functional units in nearly all cellular processes, and their atomic-level understanding is critical for elucidating and modulating molecular mechanisms. The Protein Data Bank (PDB) serves as the global repository for experimentally determined structures of macromolecules. …”
Get full text
Article -
18
Citing a Data Repository: A Case Study of the Protein Data Bank.
Published 2015-01-01“…The Protein Data Bank (PDB) is the worldwide repository of 3D structures of proteins, nucleic acids and complex assemblies. …”
Get full text
Article -
19
Integration of open access literature into the RCSB Protein Data Bank using BioLit
Published 2010-04-01“…To exploit this opportunity we present the integration of open access literature with the RCSB Protein Data Bank (PDB).</p> <p>Results</p> <p>BioLit provides an enhanced view of articles with markup of semantic data and links to biological databases, based on the content of the article. …”
Get full text
Article -
20