The Protein Data Bank

Berman, Helen M.; Battistuz, Tammy; Bhat, Talapady N.; Bluhm, Wolfgang F.; Bourne, Philip E.; Burkhardt, Kyle; Feng, Zhang; Gilliland, Gary L.; Iype, Lisa; Jain, Shri C.; Fagan, Phoebe; Marvin, Jessica; Padilla, David; Ravichandran, V.; Schneider, Bohdan; Thanki, Narmada; Weissig, Helge; Westbrook, John D.; Zardecki, Christine

doi:10.1107/s0907444902003451

Cited by 3,496 publications

(3,191 citation statements)

References 21 publications

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“…In this case, the twin fraction was lower and refined to 0.05. The coordinates, structure factors, and intensities were deposited in PDB (41). Statistics describing the data and refinement are summarized in Table 1.…”

Section: Methodsmentioning

confidence: 99%

Structural and Immunologic Characterization of Ara h 1, a Major Peanut Allergen

Chruszcz

Maleki

Majorek

et al. 2011

Journal of Biological Chemistry

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Allergic reactions to peanuts and tree nuts are major causes of anaphylaxis in the United States. We compare different properties of natural and recombinant versions of Ara h 1, a major peanut allergen, through structural, immunologic, and bioinformatics analyses. Small angle x-ray scattering studies show that natural Ara h 1 forms higher molecular weight aggregates in solution. In contrast, the full-length recombinant protein is partially unfolded and exists as a monomer. The crystal structure of the Ara h 1 core (residues 170 -586) shows that the central part of the allergen has a bicupin fold, which is in agreement with our bioinformatics analysis. In its crystalline state, the core region of Ara h 1 forms trimeric assemblies, while in solution the protein exists as higher molecular weight assemblies. This finding reveals that the residues forming the core region of the protein are sufficient for formation of Ara h 1 trimers and higher order oligomers. Natural and recombinant variants of proteins tested in in vitro gastric and duodenal digestion assays show that the natural protein is the most stable form, followed by the recombinant Ara h 1 core fragment and the full-length recombinant protein. Additionally, IgE binding studies reveal that the natural and recombinant allergens have different patterns of interaction with IgE antibodies. The molecular basis of cross-reactivity between vicilin allergens is also elucidated.

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Section: Methodsmentioning

confidence: 99%

Structural and Immunologic Characterization of Ara h 1, a Major Peanut Allergen

Chruszcz

Maleki

Majorek

et al. 2011

Journal of Biological Chemistry

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show abstract

“…Initial phases for BphB B-356 were obtained by molecular replacement using MOLREP from the CCP4 version 6.0 software suite (20). The crystal structure of BphB LB400 was used as a search model (Protein Data Bank (PDB) code 1BDB) (21). Rigid body refinement was followed by iterative cycles of restrained atomic parameter refinement using the programs CNS (22) and REFMAC_5.2 (23).…”

Section: Methodsmentioning

confidence: 99%

Biochemical Studies and Ligand-bound Structures of Biphenyl Dehydrogenase from Pandoraea pnomenusa Strain B-356 Reveal a Basis for Broad Specificity of the Enzyme

Dhindwal

Patil

Mohammadi

et al. 2011

Journal of Biological Chemistry

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Background: BphB B-356 catalyzes the second step of the PCB catabolic pathway. Result: Apo, binary, intermediate, and ternary structures were obtained. Conclusion: Conformational changes in the substrate binding loop lead to the formation of a structurally defined pocket to catalyze a wide range of substrates. Significance: Recognition of conformational changes in the substrate binding loop and insight into the substrate specificity.

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“…The popular structure-based approaches require the availability of a 3D structure for the biological target of interest, this information permitting the use of methods based on de novo design or ligand-protein docking [5][6][7], these methods becoming widely used with the continuing growth in the availability of 3D protein data [8,9]. If the necessary 3D information is not available then it may be possible to identify the structural requirements for activity by analysis of those structures that have already been shown to be active.…”

Section: Introductionmentioning

confidence: 99%

Evaluation of machine-learning methods for ligand-based virtual screening

Chen

Harrison

Papadatos

et al. 2007

J Comput Aided Mol Des

110

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Abstract. Machine-learning methods can be used for virtual screening by analysing the structural characteristics of molecules of known (in)activity, and we here discuss the use of kernel discrimination and naive Bayesian classifier methods for this purpose. We report a kernel method that allows the processing of molecules represented by binary, integer and real-valued descriptors, and show that it is little different in screening performance from a previously described kernel that had been developed specifically for the analysis of binary fingerprint representations of molecular structure. We then evaluate the performance of a naive Bayesian classifier when the training-set contains only a very few active molecules. In such cases, a simpler approach based on group fusion would appear to provide superior screening performance, especially when structurally heterogeneous datasets are to be processed.

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The Protein Data Bank

Cited by 3,496 publications

References 21 publications

Structural and Immunologic Characterization of Ara h 1, a Major Peanut Allergen

Structural and Immunologic Characterization of Ara h 1, a Major Peanut Allergen

Biochemical Studies and Ligand-bound Structures of Biphenyl Dehydrogenase from Pandoraea pnomenusa Strain B-356 Reveal a Basis for Broad Specificity of the Enzyme

Evaluation of machine-learning methods for ligand-based virtual screening

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