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  • 91
    Brookhaven Instruments protein data bank pdb
    Correlation between β -sheet stability and interresidue interactions involving the Asp-178 residue in hPrP at pH 4.5 and 7.0. The data have been obtained analyzing the 20 <t>NMR</t> conformers reported in the <t>PDB</t> for each pH (PDB codes 1QM3 and 1HJN for pH 4.5 and 7.0, respectively). The conformer numbering of the PDB files has been used. Solid and open circles refer to pH 4.5 and 7.0, respectively. In the header of the PDB file, the conformer 12 at pH 4.5 is indicated as the most representative one ( asterisk in the panels). No representative conformer has been indicated for hPrP at pH 7.0. ( a ) m ) showing the β -sheet stability. ( b ) OD-OH distance (see text for the label definition) showing the interaction between Asp-178 and Tyr-128 residues. ( c ) OD-CZ distance (see text for the label definition) showing the interaction between Asp-178 and Arg-164 residues.
    Protein Data Bank Pdb, supplied by Brookhaven Instruments, used in various techniques. Bioz Stars score: 91/100, based on 169 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Biotechnology Information protein data bank pdb
    In silico , Red, UbcH7; green, cbl; yellow, <t>RAG1;</t> magenta spheres, cbl zinc ions; grey spheres, RAG1 zinc ions. Protein Data Bank <t>(PDB)</t> ID for the cbl–ubcH7 co-structure is 1fbv, PDB ID for RAG1 RING is 1rmd.
    Protein Data Bank Pdb, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 91/100, based on 36 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Brookhaven Instruments rcsb brookhaven protein data bank pdb
    In silico , Red, UbcH7; green, cbl; yellow, <t>RAG1;</t> magenta spheres, cbl zinc ions; grey spheres, RAG1 zinc ions. Protein Data Bank <t>(PDB)</t> ID for the cbl–ubcH7 co-structure is 1fbv, PDB ID for RAG1 RING is 1rmd.
    Rcsb Brookhaven Protein Data Bank Pdb, supplied by Brookhaven Instruments, used in various techniques. Bioz Stars score: 85/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Brookhaven Instruments ncbi brookhaven protein data bank pdb
    In silico , Red, UbcH7; green, cbl; yellow, <t>RAG1;</t> magenta spheres, cbl zinc ions; grey spheres, RAG1 zinc ions. Protein Data Bank <t>(PDB)</t> ID for the cbl–ubcH7 co-structure is 1fbv, PDB ID for RAG1 RING is 1rmd.
    Ncbi Brookhaven Protein Data Bank Pdb, supplied by Brookhaven Instruments, used in various techniques. Bioz Stars score: 86/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    AstraZeneca new human protein data bank pdb
    In silico , Red, UbcH7; green, cbl; yellow, <t>RAG1;</t> magenta spheres, cbl zinc ions; grey spheres, RAG1 zinc ions. Protein Data Bank <t>(PDB)</t> ID for the cbl–ubcH7 co-structure is 1fbv, PDB ID for RAG1 RING is 1rmd.
    New Human Protein Data Bank Pdb, supplied by AstraZeneca, used in various techniques. Bioz Stars score: 90/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Gallus BioPharmaceuticals protein data bank pdb id code 1ubv
    In silico , Red, UbcH7; green, cbl; yellow, <t>RAG1;</t> magenta spheres, cbl zinc ions; grey spheres, RAG1 zinc ions. Protein Data Bank <t>(PDB)</t> ID for the cbl–ubcH7 co-structure is 1fbv, PDB ID for RAG1 RING is 1rmd.
    Protein Data Bank Pdb Id Code 1ubv, supplied by Gallus BioPharmaceuticals, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Astex protein data bank pdb accession code 4b2d declaration
    In silico , Red, UbcH7; green, cbl; yellow, <t>RAG1;</t> magenta spheres, cbl zinc ions; grey spheres, RAG1 zinc ions. Protein Data Bank <t>(PDB)</t> ID for the cbl–ubcH7 co-structure is 1fbv, PDB ID for RAG1 RING is 1rmd.
    Protein Data Bank Pdb Accession Code 4b2d Declaration, supplied by Astex, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Accelrys protein data bank pdb format
    In silico , Red, UbcH7; green, cbl; yellow, <t>RAG1;</t> magenta spheres, cbl zinc ions; grey spheres, RAG1 zinc ions. Protein Data Bank <t>(PDB)</t> ID for the cbl–ubcH7 co-structure is 1fbv, PDB ID for RAG1 RING is 1rmd.
    Protein Data Bank Pdb Format, supplied by Accelrys, used in various techniques. Bioz Stars score: 88/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Mimotopes protein data bank pdb
    The MimoPro server . Users are required to specify both the four-character identifier of an antigen structure in <t>PDB</t> database (PDB_ID) and the identifier of the interacting chain (Chain No). Users are then required to paste the <t>mimotopes</t> derived from phage display experiments. An email address should be specified and the final results will be sent through this email.
    Protein Data Bank Pdb, supplied by Mimotopes, used in various techniques. Bioz Stars score: 91/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Mine Safety Appliances protein data bank pdb
    Workflow of the study. For each query enzyme in the data set, we retrieve the structure from the <t>PDB</t> and the <t>MSA</t> from Pfam database. These are used as input for 1) GNM evaluation of residue mobilities (right branch) and 2) generation of conservation profile and coevolution maps (left branch), respectively. Comparison of the outputs shows that sequence entropy is accompanied by conformational mobility (enhanced dynamics), correlated mutations exhibit a broad range of mobilities depending on the type of underlying evolutionary pressure, and conserved sites are practically immobile. Statistically significant results are obtained by compiling the outputs for 34 enzymes.
    Protein Data Bank Pdb, supplied by Mine Safety Appliances, used in various techniques. Bioz Stars score: 91/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Biotechnology Information rcsb protein data bank pdb
    Workflow of the study. For each query enzyme in the data set, we retrieve the structure from the <t>PDB</t> and the <t>MSA</t> from Pfam database. These are used as input for 1) GNM evaluation of residue mobilities (right branch) and 2) generation of conservation profile and coevolution maps (left branch), respectively. Comparison of the outputs shows that sequence entropy is accompanied by conformational mobility (enhanced dynamics), correlated mutations exhibit a broad range of mobilities depending on the type of underlying evolutionary pressure, and conserved sites are practically immobile. Statistically significant results are obtained by compiling the outputs for 34 enzymes.
    Rcsb Protein Data Bank Pdb, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 85/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Brookhaven Instruments standard brookhaven protein data bank pdb
    Workflow of the study. For each query enzyme in the data set, we retrieve the structure from the <t>PDB</t> and the <t>MSA</t> from Pfam database. These are used as input for 1) GNM evaluation of residue mobilities (right branch) and 2) generation of conservation profile and coevolution maps (left branch), respectively. Comparison of the outputs shows that sequence entropy is accompanied by conformational mobility (enhanced dynamics), correlated mutations exhibit a broad range of mobilities depending on the type of underlying evolutionary pressure, and conserved sites are practically immobile. Statistically significant results are obtained by compiling the outputs for 34 enzymes.
    Standard Brookhaven Protein Data Bank Pdb, supplied by Brookhaven Instruments, used in various techniques. Bioz Stars score: 85/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Brookhaven Instruments β 10 brookhaven protein data bank pdb
    Workflow of the study. For each query enzyme in the data set, we retrieve the structure from the <t>PDB</t> and the <t>MSA</t> from Pfam database. These are used as input for 1) GNM evaluation of residue mobilities (right branch) and 2) generation of conservation profile and coevolution maps (left branch), respectively. Comparison of the outputs shows that sequence entropy is accompanied by conformational mobility (enhanced dynamics), correlated mutations exhibit a broad range of mobilities depending on the type of underlying evolutionary pressure, and conserved sites are practically immobile. Statistically significant results are obtained by compiling the outputs for 34 enzymes.
    β 10 Brookhaven Protein Data Bank Pdb, supplied by Brookhaven Instruments, used in various techniques. Bioz Stars score: 85/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Correlation between β -sheet stability and interresidue interactions involving the Asp-178 residue in hPrP at pH 4.5 and 7.0. The data have been obtained analyzing the 20 NMR conformers reported in the PDB for each pH (PDB codes 1QM3 and 1HJN for pH 4.5 and 7.0, respectively). The conformer numbering of the PDB files has been used. Solid and open circles refer to pH 4.5 and 7.0, respectively. In the header of the PDB file, the conformer 12 at pH 4.5 is indicated as the most representative one ( asterisk in the panels). No representative conformer has been indicated for hPrP at pH 7.0. ( a ) m ) showing the β -sheet stability. ( b ) OD-OH distance (see text for the label definition) showing the interaction between Asp-178 and Tyr-128 residues. ( c ) OD-CZ distance (see text for the label definition) showing the interaction between Asp-178 and Arg-164 residues.

    Journal: Biophysical Journal

    Article Title: Misfolding Pathways of the Prion Protein Probed by Molecular Dynamics Simulations

    doi: 10.1529/biophysj.104.049882

    Figure Lengend Snippet: Correlation between β -sheet stability and interresidue interactions involving the Asp-178 residue in hPrP at pH 4.5 and 7.0. The data have been obtained analyzing the 20 NMR conformers reported in the PDB for each pH (PDB codes 1QM3 and 1HJN for pH 4.5 and 7.0, respectively). The conformer numbering of the PDB files has been used. Solid and open circles refer to pH 4.5 and 7.0, respectively. In the header of the PDB file, the conformer 12 at pH 4.5 is indicated as the most representative one ( asterisk in the panels). No representative conformer has been indicated for hPrP at pH 7.0. ( a ) m ) showing the β -sheet stability. ( b ) OD-OH distance (see text for the label definition) showing the interaction between Asp-178 and Tyr-128 residues. ( c ) OD-CZ distance (see text for the label definition) showing the interaction between Asp-178 and Arg-164 residues.

    Article Snippet: All the simulations presented in this article began with the mPrPC NMR structure from the Brookhaven Protein Data Bank (PDB) ( ) that contains the coordinates of the residues 124–226 (PDB code: 1AG2).

    Techniques: Nuclear Magnetic Resonance

    In silico , Red, UbcH7; green, cbl; yellow, RAG1; magenta spheres, cbl zinc ions; grey spheres, RAG1 zinc ions. Protein Data Bank (PDB) ID for the cbl–ubcH7 co-structure is 1fbv, PDB ID for RAG1 RING is 1rmd.

    Journal: Immunology

    Article Title: Correlation between recombinase activating gene 1 ubiquitin ligase activity and V(D)J recombination

    doi: 10.1111/j.1365-2567.2009.03101.x

    Figure Lengend Snippet: In silico , Red, UbcH7; green, cbl; yellow, RAG1; magenta spheres, cbl zinc ions; grey spheres, RAG1 zinc ions. Protein Data Bank (PDB) ID for the cbl–ubcH7 co-structure is 1fbv, PDB ID for RAG1 RING is 1rmd.

    Article Snippet: The interface between CDC34 and RAG1 was predicted based on in silico alignment of the RAG1 RING and cbl-UbcH7 crystal structures obtained using the Protein Data Bank (PDB) co-ordinates available from the National Center for Biotechnology Information (NCBI) structural database., Initial manual alignments allowed us to designate 32 residue pairs in equivalent positions in the two structures, and these were aligned using the least square fit protocol of the align program (Shareware).

    Techniques: In Silico

    The MimoPro server . Users are required to specify both the four-character identifier of an antigen structure in PDB database (PDB_ID) and the identifier of the interacting chain (Chain No). Users are then required to paste the mimotopes derived from phage display experiments. An email address should be specified and the final results will be sent through this email.

    Journal: BMC Bioinformatics

    Article Title: MimoPro: a more efficient Web-based tool for epitope prediction using phage display libraries

    doi: 10.1186/1471-2105-12-199

    Figure Lengend Snippet: The MimoPro server . Users are required to specify both the four-character identifier of an antigen structure in PDB database (PDB_ID) and the identifier of the interacting chain (Chain No). Users are then required to paste the mimotopes derived from phage display experiments. An email address should be specified and the final results will be sent through this email.

    Article Snippet: Therefore, the required input includes both the X-ray crystal structure of a source antigen stored in a protein data bank (PDB) [ ] and mimotopes screened from phage display experiments.

    Techniques: Derivative Assay

    Workflow of the study. For each query enzyme in the data set, we retrieve the structure from the PDB and the MSA from Pfam database. These are used as input for 1) GNM evaluation of residue mobilities (right branch) and 2) generation of conservation profile and coevolution maps (left branch), respectively. Comparison of the outputs shows that sequence entropy is accompanied by conformational mobility (enhanced dynamics), correlated mutations exhibit a broad range of mobilities depending on the type of underlying evolutionary pressure, and conserved sites are practically immobile. Statistically significant results are obtained by compiling the outputs for 34 enzymes.

    Journal: Molecular Biology and Evolution

    Article Title: Sequence Evolution Correlates with Structural Dynamics

    doi: 10.1093/molbev/mss097

    Figure Lengend Snippet: Workflow of the study. For each query enzyme in the data set, we retrieve the structure from the PDB and the MSA from Pfam database. These are used as input for 1) GNM evaluation of residue mobilities (right branch) and 2) generation of conservation profile and coevolution maps (left branch), respectively. Comparison of the outputs shows that sequence entropy is accompanied by conformational mobility (enhanced dynamics), correlated mutations exhibit a broad range of mobilities depending on the type of underlying evolutionary pressure, and conserved sites are practically immobile. Statistically significant results are obtained by compiling the outputs for 34 enzymes.

    Article Snippet: For each enzyme, the multiple sequence alignment (MSA) retrieved from the Pfam database ( ) was refined using the following procedure: 1) iteratively align the primary (query) sequence from the Protein Data Bank (PDB) with each sequence in the MSA using the Smith–Waterman algorithm ( ) and identify a “matched” sequence with the highest score, which shares at least 95% sequence identity the PDB sequence; 2) based on the residue mapping between the PDB sequence and the matched sequence, truncate the columns of the MSA so as to retain those residues structurally resolved in the PDB sequence; and 3) remove the redundant sequences in the refined MSA using a threshold of 99% and eliminate the sequences that have more than 20% gaps.

    Techniques: Sequencing