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Biotechnology Information pdb protein data bank
Pdb Protein Data Bank, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Sequencing:

Article Title: In Silico Structural, Functional, and Phylogenetic Analysis of Cytochrome (CYPD) Protein Family
Article Snippet: .. Exploration and Mining of Human and Mouse CYP2D Structure and Sequences The human CYP2D gene family's amino acid sequence was searched from the Public Database of the National Center for Biotechnology Information (NCBI) https://www.ncbi.nlm.nih.gov , and the protein crystal structure was obtained from the Public Database of Protein Data Bank (PDB) http://www.rcsb.org . ..

Article Title: Genome-wide analysis of the apple CaCA superfamily reveals that MdCAX proteins are involved in the abiotic stress response as calcium transporters
Article Snippet: .. Sequence comparison and prediction of the three-dimensional structure of MdCAX proteins The protein sequence of ScVCX1 was obtained from the National Center for Biotechnology Information database (NCBI, https://www.ncbi.nlm.nih.gov/ ), and its crystallographic structure template (4k1c.pdb) was downloaded from the Protein Data Bank database (PDB, https://www.rcsb.org/ ). .. Sequence alignment was carried out with DNAMAN software (version 6).

Article Title: Combinatorial therapeutic trial plans for COVID-19 treatment armed up with antiviral, antiparasitic, cell-entry inhibitor, and immune-boosters
Article Snippet: .. Collection of data and downloading the structures Whole genome sequence of SARS-CoV-2 has been collected from National Center for Biotechnology Information (NCBI) ( https://www.ncbi.nlm.nih.gov/nuccore/NC_045512 ). ..

Article Title: Discovery and synthetic optimization of a novel scaffold for hydrophobic tunnel-targeted autotaxin inhibition
Article Snippet: Thirty-six compounds inhibited ATX-catalyzed FS-3 hydrolysis by 50% or greater at a concentration of 10 μM, with one compound having a sub-micromolar potency. .. To compare known ATX structures and to prepare a useful template for structure-based pharmacophore development for AXT inhibition, crystal structures of mouse (PDB ID: 3NKM[ ] and rat (PDB ID: 2XR9[ ]) ATX were downloaded from the Protein Data Bank (PDB[ ]) and the FASTA sequence of human ATX ( ) was obtained from the National Center for Biotechnology Information. .. [ ] Since the human ATX sequences show high sequence similarity to the mouse (95%) and rat (94%) homologues, the available mouse and rat structures were carefully scrutinized using MOE (Molecular Operating Environment, Chemical Computing Group, Montreal, Canada).

In Silico:

Article Title: Correlation between recombinase activating gene 1 ubiquitin ligase activity and V(D)J recombination
Article Snippet: Agarose gels and western blots were digitally captured using a Kodak Image Station 2000MM for 30 seconds with zero binning and quantified using kodak . .. 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). ..

Inhibition:

Article Title: Discovery and synthetic optimization of a novel scaffold for hydrophobic tunnel-targeted autotaxin inhibition
Article Snippet: Thirty-six compounds inhibited ATX-catalyzed FS-3 hydrolysis by 50% or greater at a concentration of 10 μM, with one compound having a sub-micromolar potency. .. To compare known ATX structures and to prepare a useful template for structure-based pharmacophore development for AXT inhibition, crystal structures of mouse (PDB ID: 3NKM[ ] and rat (PDB ID: 2XR9[ ]) ATX were downloaded from the Protein Data Bank (PDB[ ]) and the FASTA sequence of human ATX ( ) was obtained from the National Center for Biotechnology Information. .. [ ] Since the human ATX sequences show high sequence similarity to the mouse (95%) and rat (94%) homologues, the available mouse and rat structures were carefully scrutinized using MOE (Molecular Operating Environment, Chemical Computing Group, Montreal, Canada).

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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: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/protein data bank pdb/product/Biotechnology Information
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    protein data bank pdb - by Bioz Stars, 2021-06
    86/100 stars
      Buy from Supplier

    86
    Biotechnology Information pdb protein data bank
    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.
    Pdb Protein Data Bank, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/pdb protein data bank/product/Biotechnology Information
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    pdb protein data bank - by Bioz Stars, 2021-06
    86/100 stars
      Buy from Supplier

    86
    Biotechnology Information pdb plus swissprot plus pir plus prf
    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.
    Pdb Plus Swissprot Plus Pir Plus Prf, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/pdb plus swissprot plus pir plus prf/product/Biotechnology Information
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    pdb plus swissprot plus pir plus prf - by Bioz Stars, 2021-06
    86/100 stars
      Buy from Supplier

    Image Search Results


    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

    Overlay of the protein structures of human cathepsin V, PDB 1FH0 [ 26 ] (red ribbon), and the homology model of Trichomonas vaginalis cathepsin L-like protein, TvCPCAC1 (blue ribbon). The co-crystallized ligand is shown as a wireframe structure.

    Journal: Scientia Pharmaceutica

    Article Title: Natural Products as New Treatment Options for Trichomoniasis: A Molecular Docking Investigation

    doi: 10.3390/scipharm85010005

    Figure Lengend Snippet: Overlay of the protein structures of human cathepsin V, PDB 1FH0 [ 26 ] (red ribbon), and the homology model of Trichomonas vaginalis cathepsin L-like protein, TvCPCAC1 (blue ribbon). The co-crystallized ligand is shown as a wireframe structure.

    Article Snippet: Homology Modeling Homology models for each of the Trichomonas proteins that are not currently available from the Protein Data Bank (PDB) were constructed from crystal structure templates found in the Protein Data Bank using FASTA sequences downloaded from the National Center for Biotechnology Information’s (NCBI) GenBank.

    Techniques:

    Overlay of the protein structures of Brucella melitensis TxR, PDB 4JNQ [ 24 ] (red ribbon), and the homology model of Trichomonas vaginalis TxR (blue ribbon). The co-crystallized ligand is shown as a wireframe structure.

    Journal: Scientia Pharmaceutica

    Article Title: Natural Products as New Treatment Options for Trichomoniasis: A Molecular Docking Investigation

    doi: 10.3390/scipharm85010005

    Figure Lengend Snippet: Overlay of the protein structures of Brucella melitensis TxR, PDB 4JNQ [ 24 ] (red ribbon), and the homology model of Trichomonas vaginalis TxR (blue ribbon). The co-crystallized ligand is shown as a wireframe structure.

    Article Snippet: Homology Modeling Homology models for each of the Trichomonas proteins that are not currently available from the Protein Data Bank (PDB) were constructed from crystal structure templates found in the Protein Data Bank using FASTA sequences downloaded from the National Center for Biotechnology Information’s (NCBI) GenBank.

    Techniques:

    Ramachandran plots of cathepsin V-like protein structures: ( a ) human cathepsin V (HsCatV, PDB 1FH0 [ 26 ]); ( b ) homology model of Trichomonas vaginalis cathepsin L-like protein, TvCPCAC1; ( c ) binding site of HsCatV; ( d ) binding site of TvCPCAC1.

    Journal: Scientia Pharmaceutica

    Article Title: Natural Products as New Treatment Options for Trichomoniasis: A Molecular Docking Investigation

    doi: 10.3390/scipharm85010005

    Figure Lengend Snippet: Ramachandran plots of cathepsin V-like protein structures: ( a ) human cathepsin V (HsCatV, PDB 1FH0 [ 26 ]); ( b ) homology model of Trichomonas vaginalis cathepsin L-like protein, TvCPCAC1; ( c ) binding site of HsCatV; ( d ) binding site of TvCPCAC1.

    Article Snippet: Homology Modeling Homology models for each of the Trichomonas proteins that are not currently available from the Protein Data Bank (PDB) were constructed from crystal structure templates found in the Protein Data Bank using FASTA sequences downloaded from the National Center for Biotechnology Information’s (NCBI) GenBank.

    Techniques: Binding Assay

    Ramachandran plots of cathepsin K-like protein structures: ( a ) rabbit ( Oryctolagus cuniculus ) cathepsin K (OcCatK, PDB 2F7D [ 25 ]); ( b ) homology model of Trichomonas vaginalis papain-like protein, TvCP2; ( c ) binding site of OcCatK; ( d ) binding site of TvCP2.

    Journal: Scientia Pharmaceutica

    Article Title: Natural Products as New Treatment Options for Trichomoniasis: A Molecular Docking Investigation

    doi: 10.3390/scipharm85010005

    Figure Lengend Snippet: Ramachandran plots of cathepsin K-like protein structures: ( a ) rabbit ( Oryctolagus cuniculus ) cathepsin K (OcCatK, PDB 2F7D [ 25 ]); ( b ) homology model of Trichomonas vaginalis papain-like protein, TvCP2; ( c ) binding site of OcCatK; ( d ) binding site of TvCP2.

    Article Snippet: Homology Modeling Homology models for each of the Trichomonas proteins that are not currently available from the Protein Data Bank (PDB) were constructed from crystal structure templates found in the Protein Data Bank using FASTA sequences downloaded from the National Center for Biotechnology Information’s (NCBI) GenBank.

    Techniques: Binding Assay

    Lowest-energy re-docked poses of co-crystallized ligands: ( a ) Trichomonas vaginalis methionine gamma-lyase (TvMGL, PDB 1E5F [ 27 ]) showing the co-crystallized ligand, pyridoxal-5′-phosphate (green), and the re-docked ligand (magenta); ( b ) T. vaginalis purine nucleoside phosphorylase (TvPNP, PDB 1Z36 [ 28 ]) showing the co-crystallized ligand, (1 S )-1-(7-amino-1 H -pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro- d -ribitol (green), and the re-docked ligand (red); ( c ) human cathepsin K (HsCatK, PDB 1U9V [ 38 ]) showing the co-crystallized ligand, 6-(cyclohexylamino)-9-[2-(4-methylpiperazin-1-yl)-ethyl]-9 H -purine-2-carbonitrile (green), and the re-docked ligand (blue); and ( d ) human cathepsin L (HsCatL, PDB 3HWN [ 39 ]) showing the co-crystallized ligand, N -α-[(3- t -Butyl-1-methyl-1 H -pyrazol-5-yl)carbonyl]- N -[(2 E )-2-iminoethyl]-3-{5-[( Z )-iminomethyl]-1,3,4-oxadiazol-2-yl}- l -phenylalaninamide (green), and the re-docked ligand (aqua).

    Journal: Scientia Pharmaceutica

    Article Title: Natural Products as New Treatment Options for Trichomoniasis: A Molecular Docking Investigation

    doi: 10.3390/scipharm85010005

    Figure Lengend Snippet: Lowest-energy re-docked poses of co-crystallized ligands: ( a ) Trichomonas vaginalis methionine gamma-lyase (TvMGL, PDB 1E5F [ 27 ]) showing the co-crystallized ligand, pyridoxal-5′-phosphate (green), and the re-docked ligand (magenta); ( b ) T. vaginalis purine nucleoside phosphorylase (TvPNP, PDB 1Z36 [ 28 ]) showing the co-crystallized ligand, (1 S )-1-(7-amino-1 H -pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro- d -ribitol (green), and the re-docked ligand (red); ( c ) human cathepsin K (HsCatK, PDB 1U9V [ 38 ]) showing the co-crystallized ligand, 6-(cyclohexylamino)-9-[2-(4-methylpiperazin-1-yl)-ethyl]-9 H -purine-2-carbonitrile (green), and the re-docked ligand (blue); and ( d ) human cathepsin L (HsCatL, PDB 3HWN [ 39 ]) showing the co-crystallized ligand, N -α-[(3- t -Butyl-1-methyl-1 H -pyrazol-5-yl)carbonyl]- N -[(2 E )-2-iminoethyl]-3-{5-[( Z )-iminomethyl]-1,3,4-oxadiazol-2-yl}- l -phenylalaninamide (green), and the re-docked ligand (aqua).

    Article Snippet: Homology Modeling Homology models for each of the Trichomonas proteins that are not currently available from the Protein Data Bank (PDB) were constructed from crystal structure templates found in the Protein Data Bank using FASTA sequences downloaded from the National Center for Biotechnology Information’s (NCBI) GenBank.

    Techniques:

    Overlay of the protein structures of rabbit ( Oryctolagus cuniculus ) cathepsin K, PDB 2F7D [ 25 ] (red ribbon), and the homology model of Trichomonas vaginalis papain-like protein, TvCP2 (blue ribbon). The co-crystallized ligand is shown as a wireframe structure.

    Journal: Scientia Pharmaceutica

    Article Title: Natural Products as New Treatment Options for Trichomoniasis: A Molecular Docking Investigation

    doi: 10.3390/scipharm85010005

    Figure Lengend Snippet: Overlay of the protein structures of rabbit ( Oryctolagus cuniculus ) cathepsin K, PDB 2F7D [ 25 ] (red ribbon), and the homology model of Trichomonas vaginalis papain-like protein, TvCP2 (blue ribbon). The co-crystallized ligand is shown as a wireframe structure.

    Article Snippet: Homology Modeling Homology models for each of the Trichomonas proteins that are not currently available from the Protein Data Bank (PDB) were constructed from crystal structure templates found in the Protein Data Bank using FASTA sequences downloaded from the National Center for Biotechnology Information’s (NCBI) GenBank.

    Techniques: