Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces by Gorin Andrey A, Bordner Andrew J

“…A successful solution can provide additional insights into the fundamental principles of biological recognition and reduce errors in many algorithms and databases utilizing interaction information extracted from the Protein Data Bank (PDB).</p> <p>Results</p> <p>We have developed a method for identifying protein complexes in the PDB X-ray structures by a four step procedure: (1) comprehensively collecting all protein-protein interfaces; (2) clustering similar protein-protein interfaces together; (3) estimating the probability that each cluster is relevant based on a diverse set of properties; and (4) combining these scores for each PDB entry in order to predict the complex structure. …”
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Atypical structural tendencies among low-complexity domains in the Protein Data Bank proteome. by Sean M Cascarina, Mikaela R Elder, Eric D Ross

“…A variety of studies have suggested that low-complexity domains (LCDs) tend to be intrinsically disordered and are relatively rare within structured proteins in the Protein Data Bank (PDB). Although LCDs are often treated as a single class, we previously found that LCDs enriched in different amino acids can exhibit substantial differences in protein metabolism and function. …”
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SuperLigands – a database of ligand structures derived from the Protein Data Bank by Preissner Robert, Goede Andrean, Dunkel Mathias, Michalsky Elke

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Characteristics of interactions at protein segments without non-local intramolecular contacts in the Protein Data Bank. by Kota Kasahara, Shintaro Minami, Yasunori Aizawa

“…Here, we termed protein segments without non-local contacts as floating segments and sought them in tens of thousands of entries in the Protein Data Bank. As a result, we found that 0.72% of residues are in floating segments. …”
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Survey of the Intermolecular Disulfide Bonds Observed in Protein Crystal Structures Deposited in the Protein Data Bank by Oliviero Carugo

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PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank by Ibrahim Roshan Kunnakkattu, Preeti Choudhary, Lukas Pravda, Nurul Nadzirin, Oliver S. Smart, Qi Yuan, Stephen Anyango, Sreenath Nair, Mihaly Varadi, Sameer Velankar

“…Abstract While the Protein Data Bank (PDB) contains a wealth of structural information on ligands bound to macromolecules, their analysis can be challenging due to the large amount and diversity of data. …”
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Experimentally Determined Long Intrinsically Disordered Protein Regions Are Now Abundant in the Protein Data Bank by Alexander Miguel Monzon, Marco Necci, Federica Quaglia, Ian Walsh, Giuseppe Zanotti, Damiano Piovesan, Silvio C. E. Tosatto

“…Here, we describe a comprehensive and large-scale analysis of experimental LDRs for 3133 unique proteins, demonstrating an increasing coverage of intrinsic disorder in the Protein Data Bank (PDB) in the last decade. The results suggest that long missing residue regions are a good quality source to annotate intrinsically disordered regions and perform functional analysis in large data sets. …”
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Finding High-Quality Metal Ion-Centric Regions Across the Worldwide Protein Data Bank by Sen Yao, Hunter N.B. Moseley

“…As the number of macromolecular structures in the worldwide Protein Data Bank (wwPDB) continues to grow rapidly, more attention is being paid to the quality of its data, especially for use in aggregated structural and dynamics analyses. …”
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Interaction of Vanadium Complexes with Proteins: Revisiting the Reported Structures in the Protein Data Bank (PDB) since 2015 by Marino F. A. Santos, João Costa Pessoa

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PDBrenum: A webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences. by Bulat Faezov, Roland L Dunbrack

“…The Protein Data Bank (PDB) was established at Brookhaven National Laboratories in 1971 as an archive for biological macromolecular crystal structures. …”
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Mining the Protein Data Bank to Differentiate Error from Structural Variation in Clustered Static Structures: An Examination of HIV Protease by Robert McKenna, Mavis Agbandje-McKenna, Miorel-Lucian Palii, Balasubramanian Venkatakrishnan

“…The Protein Data Bank (PDB) contains over 71,000 structures. …”
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Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students by Stephen K. Burley, Helen M. Berman, Jose M. Duarte, Zukang Feng, Justin W. Flatt, Brian P. Hudson, Robert Lowe, Ezra Peisach, Dennis W. Piehl, Yana Rose, Andrej Sali, Monica Sekharan, Chenghua Shao, Brinda Vallat, Maria Voigt, John D. Westbrook, Jasmine Y. Young, Christine Zardecki

Subjects: “…Protein Data Bank…”
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RCSB Protein Data Bank: visualizing groups of experimentally determined PDB structures alongside computed structure models of proteins by Joan Segura, Yana Rose, Chunxiao Bi, Jose Duarte, Stephen K. Burley, Stephen K. Burley, Stephen K. Burley, Stephen K. Burley, Stephen K. Burley, Sebastian Bittrich

“…Equally important is the capability to efficiently summarize and visualize metadata, biological/biochemical annotations, and structural features, particularly when working with vast numbers of protein structures of both experimental origin from the Protein Data Bank (PDB) and computationally-predicted models. …”
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Characterization of Ionizable Groups’ Environments in Proteins and Protein–Ligand Complexes through a Statistical Analysis of the Protein Data Bank by Alexandre Borrel, Anne-Claude Camproux, Henri Xhaard

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Avoidable errors in deposited macromolecular structures: an impediment to efficient data mining by Zbigniew Dauter, Alexander Wlodawer, Wladek Minor, Mariusz Jaskolski, Bernhard Rupp

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Naked Metal Cations Swimming in Protein Crystals by Kristina Djinović-Carugo, Oliviero Carugo

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Is there an advantageous arrangement of aromatic residues in proteins? Statistical analysis of aromatic interactions in globular proteins by Mikhail Yu. Lobanov, Leonid B. Pereyaslavets, Ilya V. Likhachev, Bakhyt T. Matkarimov, Oxana V. Galzitskaya

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IsoStar Program Suite for Studies of Noncovalent Interactions in Crystals of Chemical Compounds by Alexander S. Novikov

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A Protein Data Bank survey reveals shortening of intermolecular hydrogen bonds in ligand-protein complexes when a halogenated ligand is an H-bond donor. by Jarosław Poznański, Anna Poznańska, David Shugar

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Strength and Character of R–X···π Interactions Involving Aromatic Amino Acid Sidechains in Protein-Ligand Complexes Derived from Crystal Structures in the Protein Data Bank by Kevin E. Riley, Khanh-An Tran

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