Dimer Interface Organization is a Main Determinant of Intermonomeric Interactions and Correlates with Evolutionary Relationships of Retroviral and Retroviral-Like Ddi1 and Ddi2 Pro... by János András Mótyán, Márió Miczi, József Tőzsér

“…In this study, we performed a comparative analysis based on the structural data currently available in Protein Data Bank (PDB) and Structural summaries of PDB entries (PDBsum) databases, with a special emphasis on the regions involved in dimerization of retroviral and retroviral-like Ddi proteases. …”
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The druggable genome: Twenty years later by Chris J. Radoux, Francesca Vianello, Jake McGreig, Nikita Desai, Anthony R. Bradley

“…More recently, the Protein Data Bank in Europe (PDBe) have built a knowledge base matching per-residue annotations with available protein structure. …”
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Variation in structural location and amino acid conservation of functional sites in protein domain families by Copley Richard R, Pils Birgit, Schultz Jörg

“…</p> <p>Results</p> <p>Functional sites were extracted from experimentally determined structural complexes from the Protein Data Bank harbouring a conserved protein domain from the SMART database. …”
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Expression, purification, crystallization and X-ray data collection for RAS and its mutants by Christian W. Johnson, Greg Buhrman, Pamela Y. Ting, John Colicelli, Carla Mattos

“…The crystal structures of the Y137E mutant (phosphorylation mimic) and of the Y137F mutant (without the hydroxyl group where phosphorylation occurs) were deposited in the Protein Data Bank with PDB codes 4XVQ (H-RASY137E) and 4XVR (H-RASY137F). …”
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RCH3···O Interactions in Biological Systems: Are They Trifurcated H-Bonds or Noncovalent Carbon Bonds? by Antonio Bauzá, Antonio Frontera

“…In this manuscript, we combine high-level ab initio calculations on some model systems (XCH3 σ-hole/H-bond donors) and a Protein Data Bank (PDB) survey to distinguish between trifurcated H-bonds and noncovalent carbon bonds in XCH3···O complexes (X = any atom or group). …”
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Crystal structure of domain of unknown function 507 (DUF507) reveals a new protein fold by Cole E. McKay, Jianlin Cheng, John J. Tanner

“…Structure-based query of the Protein Data Bank revealed no other protein with a similar tertiary structure, leading us to propose that AaDUF507 represents a new protein fold.…”
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Molecular docking of combretastatin derivatives to combat human cancer cells by Kshitij Chitnis, Jasdev Singh Tuteja, Priti Patidar

“…In the experiment, 21 derivatives of combretastatin were subjected to molecular docking for analyzing the binding interactions of the derivative with the active site using the Protein Data Bank: 3DK9 through Molegro Virtual Docker 6.0. …”
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pdb-care (PDB CArbohydrate REsidue check): a program to support annotation of complex carbohydrate structures in PDB files by von der Lieth Claus-W, Lütteke Thomas

“…The largest source of biomolecular 3D structures is the Protein Data Bank. However, about 30% of all 1663 PDB entries (version September 2003) containing carbohydrates comprise errors in glycan description. …”
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Identification of Structural Motifs Using Networks of Hydrogen-Bonded Base Interactions in RNA Crystallographic Structures by Hazrina Yusof Hamdani, Mohd Firdaus-Raih

“…In order to test this hypothesis, we conducted a search in available RNA crystallographic structures in the Protein Data Bank database using queries that searched for profiles of bases inter-connected by hydrogen bonds. …”
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Predicting the beta-trefoil fold from protein sequence data by Menke, Matthew Ewald, 1978-

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Molecular editor by Heng, Xiu Ting

“…The application enables users to read and modify molecules read from Protein Data Bank (PDB) file format. Users are able to modify molecules such as select, delete, copy, cut and paste of atoms. …”
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Recent advances in the production of proteins in insect and mammalian cells for structural biology. by Nettleship, J, Assenberg, R, Diprose, J, Rahman-Huq, N, Owens, R

“…Escherichia coli remains the dominant expression system in structural biology with nearly 90% of the structures in the Protein Data Bank (PDB) derived from proteins produced in this bacterial host. …”

The hairpin structure of the (6)F1(1)F2(2)F2 fragment from human fibronectin enhances gelatin binding. by Pickford, A, Smith, S, Staunton, D, Boyd, J, Campbell, I

“…The solution structure of the (6)F1(1)F2(2)F2 fragment from the gelatin-binding region of fibronectin has been determined (Protein Data Bank entry codes 1e88 and 1e8b). The structure reveals an extensive hydrophobic interface between the non-contiguous (6)F1 and (2)F2 modules. …”

RABDAM: Quantifying specific radiation damage in individual protein crystal structures by Shelley, K, Dixon, T, Brooks-Bartlett, J, Garman, E

“…Despite the use of cryo-cooling techniques, it is highly probable that a number of the structures deposited in the Protein Data Bank (PDB) have suffered substantial radiation damage as a result of the high flux densities of third generation synchrotron X-ray sources. …”

Anatomy of F1-ATPase powered rotation. by Martin, J, Ishmukhametov, R, Hornung, T, Ahmad, Z, Frasch, W

“…The angular velocity profile also supports a model in which rotation is powered by Van der Waals repulsive forces during the final 85° of rotation, consistent with a transition from F1 structures 2HLD1 and 1H8E (Protein Data Bank).…”

Modelling conformational flexibility of kinases in inactive states by Schwarz, D, Merget, B, Deane, C, Fulle, S

“…Compared to DFG‐in structures, DFG‐out structures are largely underrepresented in the Protein Data Bank (PDB). Thus, structure‐based drug design efforts for DFG‐out inhibitors may benefit from an efficient approach to generate an ensemble of DFG‐out structures. …”

Variation in structural location and amino acid conservation of functional sites in protein domain families by Pils, B, Copley, R, Schultz, J

“…Results: Functional sites were extracted from experimentally determined structural complexes from the Protein Data Bank harbouring a conserved protein domain from the SMART database. …”

Neural network for prediction of cysteine disulphide bridge connectivity in proteins by Bostan, Hamed

“…First, we preprocessed the datasets from Protein Data Bank (PDB) and filtered mutations and low resolution files out. …”
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Structural analysis and modeling comparison of primates dystrophin by Mohajer, Faeze Sadat

“…The used databases were NCBI, PDB (protein data bank), UniProt, and Gene bank. The data that is gathered from these databases were analyzed using multiple sequence analysis software such as BLAST, Jalview to find conserved regions in the protein among the species of interest (different kinds of primates). …”
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Polarized Raman anisotropic response of collagen in tendon: towards 3D orientation mapping of collagen in tissues. by Leonardo Galvis, John W C Dunlop, Georg Duda, Peter Fratzl, Admir Masic

“…For the theoretical study, several collagen-like triple-helical peptide crystal structures obtained from the Protein Data Bank were rotated "in plane" and "out of plane" to evaluate the role of molecular orientation on the intensity of the amide I band. …”
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