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  1. Image:AF-Q402B0-F1-model v4 AlphaFold.pdb (271 bytes)
  2. Image:AF-Q9ZF92-F1-model v4 AlphaFold.pdb (246 bytes)
  3. Image:AF-P45370-F1-model v4.pdb (69 bytes)
  4. Image:AF-Q9Z3Y1-F1-model v4 AlphaFold.pdb (214 bytes)
  5. Image:AF-Q9ZF94-F1-model v4 AlphaFold.pdb (246 bytes)
  6. Image:AF-Q9UBN7-F1-model v4 reduced.pdb (0 bytes)
  7. Group:SMART:A Physical Model of the beta-Adrenergic Receptor (6,969 bytes)
    10: ... is representative of the structure of GPCRs. By modeling the β2-adrenergic receptor, we hope to better...
    18: =<font color = 'blue'>Creating the Physical Model of the β2-adrenergic receptor</font>=
    20: ...ue' align='left' caption='Madison West SMART Team Model - β2-Adrenergic Receptor' scene='34/342633/Overa...
    22: ...coordinates for this structure as reported in the pdb file 2rh1, from the Ray Stevens laboratory at the...
    24: --- Our model represents <scene name='Hoelzer_Sandbox/Image_1/1...
  8. Image:AF-W8VY28-F1-model v4.pdb (0 bytes)
  9. Image:7tzf-7tyy-7tyf model.pdb (0 bytes)
  10. Image:AF-Q9UBN7-F1-model v4.pdb (0 bytes)
  11. User:Karsten Theis/T7RNAP physical model explanation (3,838 bytes)
    1: ... a physical model of the T7 virus RNA polymerase (PDB ID [[1msw]]).
    4: Above is a photograph of the two parts of the model. To assemble it, you bring the two flat sides tog...
    50: ... exiting template DNA (blue) on the right. As the model rotates, the active site comes into view. In red,...
  12. Image:Syn.PCC7002 MODEL.pdb (135 bytes)
    2: Homology model of Phosphoenolpyruvate carboxylase from Synechoco...
  13. Image:AF-P33749-F1-model v1.pdb (14 bytes)
  14. Image:HCMV Model Poster.jpg (0 bytes)
  15. Image:AF-P33748-F1-model v1.pdb (14 bytes)
  16. Category:Model compound (45 bytes)
    1: List of pages with the keyword Model compound
  17. Category:Synthetic protein model (54 bytes)
    1: List of pages with the keyword Synthetic protein model
  18. Category:Low resolution model (51 bytes)
    1: List of pages with the keyword Low resolution model
  19. Category:Hydrophilic amphipathic basic helix peptide model (80 bytes)
    1: ...yword Hydrophilic amphipathic basic helix peptide model
  20. Category:Hydrophilic amphipathic basic helix model (72 bytes)
    1: ...h the keyword Hydrophilic amphipathic basic helix model

Page text matches

  1. Hemoglobin (19,366 bytes)
    28: ...ue' align='right' caption='Human deoxyhemoglobin (PDB code [[3hhb]])'/> -->
    57: ...oxy form; and finally a summary overview. (from PDB files bio3HHB and bio1HCO)
    73: ...of Hemoglobin at The MSOE Center for BioMolecular Modeling==
    77: ... [http://proteopedia.org/wiki/index.php/1a3n 1a3n.pdb]. The two alpha-globin chains are colored light r...
    129: ... http://mgl.scripps.edu/people/goodsell/pdb/pdb41/pdb41_1.html'''
  2. 117e (5,307 bytes)
    6: ... id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="meth...
    7: ...d=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
    8: ...Bsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=117e ProSAT]</span></td></tr>
    20: ...://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=117e ConSurf].
    24: ...The D117E variant structure likewise supports our model of catalysis, as the Glu117 variant carboxylate g...
  3. Scene authoring tools (23,035 bytes)
    11: Insert PDB code or filename here' size='350' frame='true' al...
    38: ...e load button. The file will be fetched from the PDB database.
    40: To load a file that is not part of the PDB, first upload the file to Proteopedia at [[Specia...
    46: ... used to '''filter''' which atoms of the original model will be either loaded or ignored.
    76: ...lfur atoms in cysteine residues of chain B of the model by entering those specifications (see input in pi...
  4. 1e47 (4,543 bytes)
    6: ... id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="meth...
    7: ...ligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
    8: ...Bsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e47 ProSAT]</span></td></tr>
    20: ...://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1e47 ConSurf].
    24: ...ulted in a model of the catalytic mechanism. This model has now been confirmed by structural analyses of ...
  5. 1e48 (4,502 bytes)
    6: ... id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="meth...
    7: ...E:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
    8: ...Bsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e48 ProSAT]</span></td></tr>
    20: ...://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1e48 ConSurf].
    24: ...ulted in a model of the catalytic mechanism. This model has now been confirmed by structural analyses of ...
  6. 1e4b (4,472 bytes)
    6: ... id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="meth...
    7: ...ligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
    8: ...Bsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e4b ProSAT]</span></td></tr>
    20: ...://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1e4b ConSurf].
    24: ...ulted in a model of the catalytic mechanism. This model has now been confirmed by structural analyses of ...
  7. 1e4i (5,527 bytes)
    6: ... id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="meth...
    7: ...-ALPHA-D-GLUCOPYRANOSE'>G2F</scene>, <scene name='pdbligand=NFG:2,4-DINITROPHENYL+2-DEOXY-2-FLUORO-BETA...
    8: ...Bsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e4i ProSAT]</span></td></tr>
    20: ...://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1e4i ConSurf].
    24: ...sidase A from Bacillus polymyxa is an interesting model for studies of protein engineering. This is a wel...
  8. 1e46 (4,472 bytes)
    6: ... id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="meth...
    7: ...ligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
    8: ...Bsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e46 ProSAT]</span></td></tr>
    20: ...://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1e46 ConSurf].
    24: ...ulted in a model of the catalytic mechanism. This model has now been confirmed by structural analyses of ...
  9. 1e4c (4,472 bytes)
    6: ... id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="meth...
    7: ...ligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
    8: ...Bsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e4c ProSAT]</span></td></tr>
    20: ...://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1e4c ConSurf].
    24: ...ulted in a model of the catalytic mechanism. This model has now been confirmed by structural analyses of ...
  10. 2lxy (3,569 bytes)
    6: ...class="sblockDat" id="methodDat">Solution NMR, 32 models</td></tr>
    7: ...<td class="sblockDat" id="ligandDat"><scene name='pdbligand=HTS:2-MERCAPTOPHENOL'>HTS</scene></td></tr>
    8: ...Bsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lxy ProSAT]</span></td></tr>
    12: ...tes that the synthetic 2-mercaptophenol-alpha(3)C model protein behaves structurally as a natural protein...
    18: <div class="pdbe-citations 2lxy" style="background-color:#fffaf0;...
  11. 1e49 (4,477 bytes)
    6: ... id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="meth...
    7: ...ligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
    8: ...Bsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e49 ProSAT]</span></td></tr>
    20: ...://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1e49 ConSurf].
    24: ...ulted in a model of the catalytic mechanism. This model has now been confirmed by structural analyses of ...
  12. 1e4a (4,475 bytes)
    6: ... id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="meth...
    7: ...ligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
    8: ...Bsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e4a ProSAT]</span></td></tr>
    20: ...://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1e4a ConSurf].
    24: ...ulted in a model of the catalytic mechanism. This model has now been confirmed by structural analyses of ...
  13. 1vyw (7,803 bytes)
    6: ... id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="meth...
    7: ...-(2-NAPHTHYL)ACETAMIDE'>292</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
    8: ...Bsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vyw ProSAT]</span></td></tr>
    20: ...://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1vyw ConSurf].
    24: ...umor activity (TGI &gt; 50%) in a mouse xenograft model at a dose devoid of toxic effects.
  14. 1vyz (7,690 bytes)
    6: ... id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="meth...
    7: ...<td class="sblockDat" id="ligandDat"><scene name='pdbligand=N5B:N-(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)BENZAM...
    8: ...Bsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vyz ProSAT]</span></td></tr>
    20: ...://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1vyz ConSurf].
    24: ...umor activity (TGI &gt; 50%) in a mouse xenograft model at a dose devoid of toxic effects.
  15. Sandbox 781 (8,140 bytes)
    35: ...e, 6OYH, serve as a generalizable MraY structural model to study and better understand the action of the ...
  16. 2boy (5,193 bytes)
    6: ... id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="meth...
    7: ...YL]ETHYL+HEXADECANOATE'>LPP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
    8: ...Bsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2boy ProSAT]</span></td></tr>
    20: ...://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2boy ConSurf].
    24: ...m the same organism (PDB code 1S9A) as a starting model and refined at 1.9 A resolution (R(free) 21.9%; R...
  17. 2bou (5,168 bytes)
    6: ... id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="meth...
    7: ...dbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene></td></tr>
    8: ...Bsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bou ProSAT]</span></td></tr>
    22: ...://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2bou ConSurf].
    26: ...MR2-CD55 interaction has allowed us to generate a model for the CD97-CD55 complex. The structure of the c...
  18. 2boq (5,896 bytes)
    6: ... id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="meth...
    7: ...d=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
    8: ...Bsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2boq ProSAT]</span></td></tr>
    20: ...://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2boq ConSurf].
    24: ...equired for oxidation of two high redox potential model substrates (veratryl alcohol and Reactive Black 5...
  19. 2bo2 (5,119 bytes)
    6: ... id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="meth...
    7: ...dbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene></td></tr>
    8: ...Bsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bo2 ProSAT]</span></td></tr>
    22: ...://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2bo2 ConSurf].
    26: ...MR2-CD55 interaction has allowed us to generate a model for the CD97-CD55 complex. The structure of the c...
  20. 1boh (5,329 bytes)
    6: ... id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="meth...
    7: ...<td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</scene></td></t...
    8: ...Bsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1boh ProSAT]</span></td></tr>
    20: ...://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1boh ConSurf].
    24: ...by the crystal environment. The results support a model in which loss of interactions near the rhodanese ...

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